diff --git a/.gitignore b/.gitignore index a56646eb2..3c07ee7fb 100644 --- a/.gitignore +++ b/.gitignore @@ -40,3 +40,4 @@ target # JBrowse /Model/lib/jbrowse/auto_generated/ +.worktrees diff --git a/Model/lib/jbrowse/aalbSTECLA/tracks.conf b/Model/lib/jbrowse/aalbSTECLA/tracks.conf index 3812a94fe..3b309ce97 100644 --- a/Model/lib/jbrowse/aalbSTECLA/tracks.conf +++ b/Model/lib/jbrowse/aalbSTECLA/tracks.conf @@ -1,11 +1,8 @@ [tracks.aalbSTECLA_bld54Transcripts_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='aalbSTECLA_bld54Transcripts_transcript_sequences_RSRC' category=Gene Models key=Anopheles albimanus STECLA build 54 models -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=AalbimanusSTECLA/alignedTranscripts/gff/aalbSTECLA_bld54Transcripts_transcript_sequences_RSRC/aalbSTECLA_bld54Transcripts_transcript_sequences_RSRC.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript style.utrColor=grey diff --git a/Model/lib/jbrowse/acasNeff/tracks.conf b/Model/lib/jbrowse/acasNeff/tracks.conf index 6bbe540f0..2fee6b733 100644 --- a/Model/lib/jbrowse/acasNeff/tracks.conf +++ b/Model/lib/jbrowse/acasNeff/tracks.conf @@ -1,11 +1,8 @@ [tracks.acasNeff_bld56Transcripts_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='acasNeff_bld56Transcripts_transcript_sequences_RSRC' category=Gene Models key=Transcripts for build 56 models -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=AcastellaniiNeff/alignedTranscripts/gff/acasNeff_bld56Transcripts_transcript_sequences_RSRC/acasNeff_bld56Transcripts_transcript_sequences_RSRC.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript style.utrColor=grey diff --git a/Model/lib/jbrowse/acolNgousso/tracks.conf b/Model/lib/jbrowse/acolNgousso/tracks.conf index a93b374b7..1feb6defe 100644 --- a/Model/lib/jbrowse/acolNgousso/tracks.conf +++ b/Model/lib/jbrowse/acolNgousso/tracks.conf @@ -1,11 +1,8 @@ [tracks.acolNgousso_bld54Transcripts_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='acolNgousso_bld54Transcripts_transcript_sequences_RSRC' category=Gene Models key=Anopheles coluzzii Ngousso build 54 models -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=AcoluzziiNgousso/alignedTranscripts/gff/acolNgousso_bld54Transcripts_transcript_sequences_RSRC/acolNgousso_bld54Transcripts_transcript_sequences_RSRC.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript style.utrColor=grey diff --git a/Model/lib/jbrowse/afumA1163/tracks.conf b/Model/lib/jbrowse/afumA1163/tracks.conf index c723016bb..cb5f74935 100644 --- a/Model/lib/jbrowse/afumA1163/tracks.conf +++ b/Model/lib/jbrowse/afumA1163/tracks.conf @@ -1,12 +1,10 @@ # [tracks.afumA1163_Weaver_lncRNA_GFF_RSRC] -# query.feature=gff:basic -# query.edName='afumA1163_Weaver_lncRNA_GFF_RSRC' # category=Gene Models # metadata.subcategory=Transcripts # metadata.trackType=Segments -# storeClass=JBrowse/Store/SeqFeature/REST +# storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +# urlTemplate=/a/service/jbrowse/store?data=AfumigatusA1163/prealigned/gff/afumA1163_Weaver_lncRNA_WebService_RSRC/afumA1163_Weaver_lncRNA.gff.gz # style.color={processedTranscriptColor} -# baseUrl=/a/service/jbrowse # type=JBrowse/View/Track/CanvasFeatures # glyph=JBrowse/View/FeatureGlyph/Box # style.strandArrow=false diff --git a/Model/lib/jbrowse/afunidAnoFuneDA416_04/tracks.conf b/Model/lib/jbrowse/afunidAnoFuneDA416_04/tracks.conf index 3fa9b3fc1..5c85536bd 100644 --- a/Model/lib/jbrowse/afunidAnoFuneDA416_04/tracks.conf +++ b/Model/lib/jbrowse/afunidAnoFuneDA416_04/tracks.conf @@ -1,19 +1,22 @@ [tracks.afunidAnoFuneDA416_04_FUMOZ_liftoff_phase_corrected_GFF_RSRC] -query.feature=gff:processedTranscript -query.edName='afunidAnoFuneDA416_04_FUMOZ_liftoff_phase_corrected_GFF_RSRC' category=Gene Models metadata.subcategory=Transcripts metadata.trackType=Processed Transcript -storeClass=JBrowse/Store/SeqFeature/REST +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=AfunestusAfunGA1/prealigned/gff/afunidAnoFuneDA416_04_FUMOZ_liftoff_phase_corrected_WebService_RSRC/afunidAnoFuneDA416_04_FUMOZ_liftoff_phase_corrected.gff.gz +type=NeatCanvasFeatures/View/Track/NeatFeatures +glyph=NeatCanvasFeatures/View/FeatureGlyph/Gene +transcriptType={geneTranscriptType} +noncodingType=nc_transcript +labelTranscripts=false +unsafePopup="JSON::true" style.color={liftoffTranscriptColor} style.borderColor={processedTranscriptBorderColor} style.utrColor=grey -baseUrl=/a/service/jbrowse -#glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript -type=NeatCanvasFeatures/View/Track/NeatFeatures +style.topLevelFeaturesPercent=10 +style.labelScale=0.01 key=Liftoff Gene models of FUMOZ to AfunGA1 -unsafePopup="JSON::true" onClick.content={liftoffGeneDetails} metadata.dataset= fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("afunidAnoFuneDA416_04_FUMOZ_liftoff_phase_corrected_GFF_RSRC", "Liftoff Gene models of FUMOZ to AfunGA1"); } diff --git a/Model/lib/jbrowse/agamIfakara/tracks.conf b/Model/lib/jbrowse/agamIfakara/tracks.conf index fae7726e5..b36b527de 100644 --- a/Model/lib/jbrowse/agamIfakara/tracks.conf +++ b/Model/lib/jbrowse/agamIfakara/tracks.conf @@ -1,22 +1,24 @@ [tracks.agamIfakara_GCAv1_to_GCFv2_GFF_RSRC] -query.feature=gff:processedTranscript -query.edName='agamIfakara_GCAv1_to_GCFv2_GFF_RSRC' category=Gene Models -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/CanvasFeatures -glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript +key=Annotation produced by the Ensembl genebuild +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=AgambiaeIfakara/prealigned/gff/agamIfakara_GCAv1_to_GCFv2_WebService_RSRC/agamIfakara_GCAv1_to_GCFv2.gff.gz +type=NeatCanvasFeatures/View/Track/NeatFeatures +glyph=NeatCanvasFeatures/View/FeatureGlyph/Gene +transcriptType={geneTranscriptType} +noncodingType=nc_transcript +labelTranscripts=false +unsafePopup="JSON::true" style.color={alternateTranscriptColor} +style.borderColor={processedTranscriptBorderColor} style.utrColor=grey +style.topLevelFeaturesPercent=10 +style.labelScale=0.01 onClick.content={gffGeneFeatureTitleFxn} menuTemplate+=json:{"label": "View Details", "content": "{gffGeneFeatureTitleFxn}"} -key=Annotation produced by the Ensembl genebuild metadata.subcategory=Transcripts metadata.trackType=Processed Transcript -metadata.description=${summary} -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("${datasetName}", "${datasetDisplayName}"); } metadata.description=Annotation produced by the Ensembl genebuild +fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("${datasetName}", "${datasetDisplayName}"); } fmtMetaValue_Description=function() { return datasetDescription("Annotation was produced by the Ensembl genebuild","")} -onClick.content={DatasetFeatureTitleFxn} -menuTemplate+=json:{"label": "View Details", "content": "{gffGeneFeatureTitleFxn}"} diff --git a/Model/lib/jbrowse/anidFGSCA4/tracks.conf b/Model/lib/jbrowse/anidFGSCA4/tracks.conf index 787e0c471..ec23b6e28 100644 --- a/Model/lib/jbrowse/anidFGSCA4/tracks.conf +++ b/Model/lib/jbrowse/anidFGSCA4/tracks.conf @@ -37,20 +37,18 @@ metadata.subcategory=Transcriptional regulatory sites metadata.trackType=XYPlot [tracks.anidFGSCA4_TurnerAnnotation_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='anidFGSCA4_TurnerAnnotation_transcript_sequences_RSRC' category=Gene Models key=A. nidulans FGSC A4 (2009) Genome Sequence and Annotation -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=AnidulansFGSCA4/alignedTranscripts/gff/anidFGSCA4_TurnerAnnotation_transcript_sequences_RSRC/anidFGSCA4_TurnerAnnotation_transcript_sequences_RSRC.gff.gz +subParts=veupathdb type=JBrowse/View/Track/CanvasFeatures -glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript -style.utrColor=grey +glyph=JBrowse/View/FeatureGlyph/Segments style.color={alternateTranscriptColor} +style.label=function(feature){ return feature.get("transcriptid"); } metadata.subcategory=Transcripts metadata.trackType=Processed Transcript metadata.dataset=A. nidulans FGSC A4 (2009) Genome Sequence and Annotation fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("anidFGSCA4_TurnerAnnotation_transcript_sequences_RSRC", "A. nidulans FGSC A4 (2009) Genome Sequence and Annotation"); } menuTemplate+=json:{"label": "View Details", "content": "{sequenceTitleFxn}"} -onClick.content={sequenceTitleFxn} +onClick.content=function(track, feature){ var c = track.browser.config; return c.sequenceTitleFxn(track, feature) } diff --git a/Model/lib/jbrowse/aquaSANGWE/tracks.conf b/Model/lib/jbrowse/aquaSANGWE/tracks.conf index 2ccd5acba..b80029a91 100644 --- a/Model/lib/jbrowse/aquaSANGWE/tracks.conf +++ b/Model/lib/jbrowse/aquaSANGWE/tracks.conf @@ -1,11 +1,8 @@ [tracks.aquaSANGWE_bld54Transcripts_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='aquaSANGWE_bld54Transcripts_transcript_sequences_RSRC' category=Gene Models key=Anopheles quadriannulatus SANGWE build 54 models -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=AquadriannulatusSANGWE/alignedTranscripts/gff/aquaSANGWE_bld54Transcripts_transcript_sequences_RSRC/aquaSANGWE_bld54Transcripts_transcript_sequences_RSRC.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript style.utrColor=grey diff --git a/Model/lib/jbrowse/cimmRS/tracks.conf b/Model/lib/jbrowse/cimmRS/tracks.conf index c1979c978..c1f3c0939 100644 --- a/Model/lib/jbrowse/cimmRS/tracks.conf +++ b/Model/lib/jbrowse/cimmRS/tracks.conf @@ -1,8 +1,6 @@ [tracks.cimmRSKirklandTE] -query.feature=gff:basic -query.edName='cimmRS_Kirkland_TE_GFF_RSRC' -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=CimmitisRS/prealigned/gff/cimmRS_Kirkland_TE_WebService_RSRC/cimmRS_Kirkland_TE.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/Box key=C. immitis RS TE (Kirkland et al) diff --git a/Model/lib/jbrowse/cposC735deltSOWgp/tracks.conf b/Model/lib/jbrowse/cposC735deltSOWgp/tracks.conf index e9a4fffc7..020015489 100644 --- a/Model/lib/jbrowse/cposC735deltSOWgp/tracks.conf +++ b/Model/lib/jbrowse/cposC735deltSOWgp/tracks.conf @@ -1,8 +1,6 @@ [tracks.CposC735KirklandTE] -query.feature=gff:basic -query.edName='cposC735deltSOWgp_Kirkland_TE_GFF_RSRC' -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=CposadasiiC735deltSOWgp/prealigned/gff/cposC735deltSOWgp_Kirkland_TE_WebService_RSRC/cposC735deltSOWgp_Kirkland_TE.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/Box key=C. posadasii C735 TE (Kirkland et al) diff --git a/Model/lib/jbrowse/cquiJHB/tracks.conf b/Model/lib/jbrowse/cquiJHB/tracks.conf index f64bea8ec..20c74cdc6 100644 --- a/Model/lib/jbrowse/cquiJHB/tracks.conf +++ b/Model/lib/jbrowse/cquiJHB/tracks.conf @@ -1,11 +1,8 @@ [tracks.cquiJHB_bld65Transcripts_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='cquiJHB_bld65Transcripts_transcript_sequences_RSRC' category=Gene Models key=Culex quinquefasciatus JHB 2020 transcripts from build 65 models -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=CquinquefasciatusJHB2020/alignedTranscripts/gff/cquiJHB_bld65Transcripts_transcript_sequences_RSRC/cquiJHB_bld65Transcripts_transcript_sequences_RSRC.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript style.utrColor=grey diff --git a/Model/lib/jbrowse/edisSAW760/tracks.conf b/Model/lib/jbrowse/edisSAW760/tracks.conf index 3a5d730cd..e75be8565 100644 --- a/Model/lib/jbrowse/edisSAW760/tracks.conf +++ b/Model/lib/jbrowse/edisSAW760/tracks.conf @@ -1,15 +1,13 @@ [tracks.edisSAW760_TSS] -query.feature=gff:basic -query.edName='edisSAW760_TSS_Mornico_GFF_RSRC' category=Sequence Analysis metadata.subcategory=Sequence sites, features and motifs key=TSS Sites -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=EdisparSAW760/prealigned/gff/edisSAW760_TSS_Mornico_WebService_RSRC/edisSAW760_TSS_Mornico.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/Box metadata.dataset=Transcription start sites for E. dispar -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("edisSAW760_TSS_Mornico_GFF_RSRC", "Transcription start sites for E. dispar"); } +fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("edisSAW760_TSS_Mornico_WebService_RSRC", "Transcription start sites for E. dispar"); } style.color=black style.strandArrow=false metadata.trackType=Segments diff --git a/Model/lib/jbrowse/ehisHM1IMSS/tracks.conf b/Model/lib/jbrowse/ehisHM1IMSS/tracks.conf index 5e47895df..af4e7f751 100644 --- a/Model/lib/jbrowse/ehisHM1IMSS/tracks.conf +++ b/Model/lib/jbrowse/ehisHM1IMSS/tracks.conf @@ -20,13 +20,11 @@ region_feature_densities=true [tracks.ehisHM1IMSS_TSS] -query.feature=gff:basic -query.edName='ehisHM1IMSS_TSS_Mornico_GFF_RSRC' category=Sequence Analysis metadata.subcategory=Sequence sites, features and motifs key=TSS Sites -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=EhistolyticaHM1IMSS/prealigned/gff/ehisHM1IMSS_TSS_Mornico_WebService_RSRC/ehisHM1IMSS_TSS_Mornico.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/Box metadata.dataset=Transcription start sites for E. histolytica diff --git a/Model/lib/jbrowse/einvIP1/tracks.conf b/Model/lib/jbrowse/einvIP1/tracks.conf index 0875f2d4f..d6da6d523 100644 --- a/Model/lib/jbrowse/einvIP1/tracks.conf +++ b/Model/lib/jbrowse/einvIP1/tracks.conf @@ -1,11 +1,9 @@ [tracks.einvIP1_TSS] -query.feature=gff:basic -query.edName='einvIP1_TSS_Mornico_GFF_RSRC' category=Sequence Analysis metadata.subcategory=Sequence sites, features and motifs key=TSS Sites -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=EinvadensIP1/prealigned/gff/einvIP1_TSS_Mornico_WebService_RSRC/einvIP1_TSS_Mornico.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/Box metadata.dataset=Transcription start sites for E. invadens diff --git a/Model/lib/jbrowse/emosLaredo/tracks.conf b/Model/lib/jbrowse/emosLaredo/tracks.conf index 97adecb38..1bb224751 100644 --- a/Model/lib/jbrowse/emosLaredo/tracks.conf +++ b/Model/lib/jbrowse/emosLaredo/tracks.conf @@ -1,15 +1,13 @@ [tracks.emosLaredo_TSS] -query.feature=gff:basic -query.edName='emosLaredo_TSS_Mornico_GFF_RSRC' category=Sequence Analysis metadata.subcategory=Sequence sites, features and motifs key=TSS Sites -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=EmoshkovskiiLaredo/prealigned/gff/emosLaredo_TSS_Mornico_WebService_RSRC/emosLaredo_TSS_Mornico.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/Box metadata.dataset=Transcription start sites for E. moshkovskii -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("emosLaredo_TSS_Mornico_GFF_RSRC", "Transcription start sites for E. moshkovskii"); } +fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("emosLaredo_TSS_Mornico_WebService_RSRC", "Transcription start sites for E. moshkovskii"); } style.color=black style.strandArrow=false metadata.trackType=Segments diff --git a/Model/lib/jbrowse/functions.conf b/Model/lib/jbrowse/functions.conf index b2c5675a2..06fe6588e 100644 --- a/Model/lib/jbrowse/functions.conf +++ b/Model/lib/jbrowse/functions.conf @@ -779,6 +779,15 @@ lowComplexityDetailsFxn = function(track, feature, featureDiv) { var c = track.browser.config; return c.positionAndSequence(track, feature, featureDiv); } +transposableElementDetailsFxn = function(track, feature, featureDiv) { + var c = track.browser.config; + var rows = new Array(); + rows.push(c.twoColRow('Transposable Element:', feature.get('id'))); + rows.push(c.twoColRow('Name:', feature.get('te_name'))); + rows.push(c.twoColRow('Size:', feature.get('alignLength'))); + rows.push(c.twoColRow('Position:', feature.get('sequence_id') + ':' + (feature.get('start') + 1) + '..' + feature.get('end'))); + return c.table(rows); + } snpTitleFxn = function(track, feature, featureDiv) { var c = track.browser.config; return c.snpTitle(track, feature, featureDiv); @@ -819,6 +828,73 @@ gffGeneFeatureTitleFxn = function(track, feature) { var c = track.browser.config; return c.gffGeneFeatureTitle(track,feature) } +gffGeneFeatureTitle = function(track, feature) { + var c = track.browser.config; + var rows = new Array(); + var subfeatures = feature.get("subfeatures") || []; + var mrnas = subfeatures.filter(function(sf) { + var t = sf.get("type"); + return t === "mRNA" || t === "transcript"; + }); + var transcripts = mrnas.length > 0 ? mrnas : [feature]; + transcripts.forEach(function(mRNA) { + var transcriptId = mRNA.get("name"); + var strand = mRNA.get("strand"); + var totScore = mRNA.get("score"); + var five_sample = mRNA.get("fiveutr_sample"); + var five_score = mRNA.get("fiveutr_score"); + var three_sample = mRNA.get("threeutr_sample"); + var three_score = mRNA.get("threeutr_score"); + var sfs = mRNA.get("subfeatures") || []; + var cdsSfs = sfs.filter(function(sf) { return sf.get("type") === "CDS"; }); + var fiveUtrSfs = sfs.filter(function(sf) { return sf.get("type") === "five_prime_UTR"; }); + var threeUtrSfs = sfs.filter(function(sf) { return sf.get("type") === "three_prime_UTR"; }); + cdsSfs = cdsSfs.sort(function(a,b){ return a.get("start") - b.get("start"); }); + fiveUtrSfs = fiveUtrSfs.sort(function(a,b){ return a.get("start") - b.get("start"); }); + threeUtrSfs = threeUtrSfs.sort(function(a,b){ return a.get("start") - b.get("start"); }); + var cdsStrings, fiveUtrStrings, threeUtrStrings; + if (strand == '-1') { + cdsSfs.reverse(); + fiveUtrSfs.reverse(); + threeUtrSfs.reverse(); + cdsStrings = cdsSfs.map(function(x) { return 'complement(' + x.get("end") + '..' + (x.get("start")+1) + ')'; }); + fiveUtrStrings = fiveUtrSfs.map(function(x) { return 'complement(' + x.get("end") + '..' + (x.get("start")+1) + ')'; }); + threeUtrStrings = threeUtrSfs.map(function(x) { return 'complement(' + x.get("end") + '..' + (x.get("start")+1) + ')'; }); + } else { + cdsStrings = cdsSfs.map(function(x) { return (x.get("start")+1) + '..' + x.get("end"); }); + fiveUtrStrings = fiveUtrSfs.map(function(x) { return (x.get("start")+1) + '..' + x.get("end"); }); + threeUtrStrings = threeUtrSfs.map(function(x) { return (x.get("start")+1) + '..' + x.get("end"); }); + } + if (transcriptId != null) { + rows.push(c.twoColRow('ID:', transcriptId)); + } + if (totScore != null && totScore != 'NaN') { + rows.push(c.twoColRow('Score:', totScore)); + } + if (fiveUtrStrings.length > 0) { + rows.push(c.twoColRowVAlign('5\' UTR:', fiveUtrStrings.join("
"), 'top')); + } + if (cdsStrings.length > 0) { + rows.push(c.twoColRowVAlign('CDS:', cdsStrings.join("
"), 'top')); + } + if (threeUtrStrings.length > 0) { + rows.push(c.twoColRowVAlign('3\' UTR:', threeUtrStrings.join("
"), 'top')); + } + if (five_sample != null) { + rows.push(c.twoColRow('5\' UTR Samples:', five_sample)); + } + if (five_score != null) { + rows.push(c.twoColRow('5\' UTR Scores:', five_score)); + } + if (three_sample != null) { + rows.push(c.twoColRow('3\' UTR Samples:', three_sample)); + } + if (three_score != null) { + rows.push(c.twoColRow('3\' UTR Scores:', three_score)); + } + }); + return c.table(rows); + } microsatelliteTitleFxn = function(track, feature, featDiv) { var c = track.browser.config; return c.microsatelliteTitle(track, feature, featDiv); @@ -1060,19 +1136,19 @@ interproLink = function(track, feature, featDiv) { } gffTitle = function(track, feature, featDiv) { var c = track.browser.config; - var name = feature.get("name"); + var name = feature.get("name") || feature.get("id"); var seq_id = name.replace(/_m6A/g, ''); - var start = feature.get("startm"); + var start = feature.get("start") + 1; var end = feature.get("end"); var strand = strand = feature.get("strand") == 1 ? "+" : "-"; var length = Math.abs(end - start) + 1; var rows = new Array(); rows.push(c.twoColRow('Name:', name)); rows.push(c.twoColRow('Type:', 'gff')); - rows.push(c.twoColRow('Source:', feature.get("source"))); + rows.push(c.twoColRow('Source:', feature.get("source").replace(/_/g, ' '))); rows.push(c.twoColRow('Position:', seq_id + ":" + start + ".." + end + " (" + strand + " strand)" )); rows.push(c.twoColRow('Length:', length + ' bp')); - rows.push(c.twoColRow('SO Term:', feature.get("soTerm"))); + rows.push(c.twoColRow('SO Term:', feature.get("type"))); return c.table(rows); } microsatelliteTitle = function(track, feature, featDiv) { @@ -1732,18 +1808,6 @@ gene_title_gff = function(tip, sourceId, fiveUtr, cdss, threeUtr, totScore, five }; return c.table(rows); } -gffGeneFeatureTitle = function(track, feature) { - var c = track.browser.config; - var sourceId = feature.get("name"); - var strand = feature.get("strand"); - var model = c.orientAndGetUtrsAndCDS(strand, feature.get("subfeatures"), track); - var five_sample = feature.get("fiveutr_sample"); - var five_score = feature.get("fiveutr_score"); - var three_sample = feature.get("threeutr_sample"); - var three_score = feature.get("threeutr_score"); - var totScore = feature.get("score"); - return c.gene_title_gff(this, sourceId, model[0].join("
"), model[1].join("
"), model[2].join("
"), totScore, five_sample, five_score, three_sample, three_score, track); - } orientAndGetUtrsAndCDSnew = function(strand, feature, track) { var exons = feature.get("subfeatures"); var c = track.browser.config; @@ -1988,9 +2052,9 @@ gffTssChabbert = function(track, feature) { sequenceTitle = function(track, feature) { var c = track.browser.config; var rows = new Array(); - var sourceId = feature.get("name"); + var sourceId = feature.get("transcriptId"); rows.push(c.twoColRow('ID:', sourceId)); - rows.push(c.twoColRow("Position:", c.positionNoStrandString(track.refSeq.name, feature.get("startm"), feature.get("end")))); + rows.push(c.twoColRow("Position:", c.positionNoStrandString(track.refSeq.name, feature.get("start"), feature.get("end")))); return c.table(rows); } processedTranscriptDetails = function(track, feature, featureDiv) { diff --git a/Model/lib/jbrowse/gfusIAEA2018/tracks.conf b/Model/lib/jbrowse/gfusIAEA2018/tracks.conf index 4585db8dc..69e3ad839 100644 --- a/Model/lib/jbrowse/gfusIAEA2018/tracks.conf +++ b/Model/lib/jbrowse/gfusIAEA2018/tracks.conf @@ -1,11 +1,8 @@ [tracks.gfusIAEA2018_bld65Transcripts_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='gfusIAEA2018_bld65Transcripts_transcript_sequences_RSRC' category=Gene Models key=Glossina fuscipes IAEA 2018 transcripts from build 65 models -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=GfuscipesIAEA2018/alignedTranscripts/gff/gfusIAEA2018_bld65Transcripts_transcript_sequences_RSRC/gfusIAEA2018_bld65Transcripts_transcript_sequences_RSRC.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript style.utrColor=grey diff --git a/Model/lib/jbrowse/gmorYale/tracks.conf b/Model/lib/jbrowse/gmorYale/tracks.conf index 326106684..65e80c3ac 100644 --- a/Model/lib/jbrowse/gmorYale/tracks.conf +++ b/Model/lib/jbrowse/gmorYale/tracks.conf @@ -1,11 +1,8 @@ [tracks.gmorYale_bld53Transcripts_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='gmorYale_bld53Transcripts_transcript_sequences_RSRC' category=Gene Models key=Glossina morsitans Yale build 53 models -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=GmorsitansYale/alignedTranscripts/gff/gmorYale_bld53Transcripts_transcript_sequences_RSRC/gmorYale_bld53Transcripts_transcript_sequences_RSRC.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript style.utrColor=grey @@ -13,6 +10,6 @@ style.color={alternateTranscriptColor} metadata.subcategory=Transcripts metadata.trackType=Processed Transcript metadata.dataset=Glossina morsitans Yale build 53 models -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("gmorYale_bld53Transcripts_transcript_sequences_RSRCz<", "Glossina morsitans Yale build 53 models"); } +fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("gmorYale_bld53Transcripts_transcript_sequences_RSRC", "Glossina morsitans Yale build 53 models"); } menuTemplate+=json:{"label": "View Details", "content": "{sequenceTitleFxn}"} onClick.content={sequenceTitleFxn} diff --git a/Model/lib/jbrowse/hcapG186AR/tracks.conf b/Model/lib/jbrowse/hcapG186AR/tracks.conf index dfe9f7715..1f8066d43 100644 --- a/Model/lib/jbrowse/hcapG186AR/tracks.conf +++ b/Model/lib/jbrowse/hcapG186AR/tracks.conf @@ -1,19 +1,16 @@ [tracks.hcapG186AR_bld63Transcripts_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='hcapG186AR_bld63Transcripts_transcript_sequences_RSRC' category=Gene Models -key=Histoplasma capsulatum G186AR transcripts from build 63 models -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +key=Histoplasma capsulatum G186AR transcripts from build 63 models +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=HcapsulatumG186AR/alignedTranscripts/gff/hcapG186AR_bld63Transcripts_transcript_sequences_RSRC/hcapG186AR_bld63Transcripts_transcript_sequences_RSRC.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript style.utrColor=grey style.color={alternateTranscriptColor} metadata.subcategory=Transcripts metadata.trackType=Processed Transcript -metadata.dataset=Histoplasma capsulatum G186AR transcripts from build 63 models -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("hcapG186AR_bld63Transcripts_transcript_sequences_RSRC", "Histoplasma capsulatum G186AR transcripts from build 63 models"); } +metadata.dataset=Histoplasma capsulatum G186AR transcripts from build 63 models +fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("hcapG186AR_bld63Transcripts_transcript_sequences_RSRC", "Histoplasma capsulatum G186AR transcripts from build 63 models"); } menuTemplate+=json:{"label": "View Details", "content": "{sequenceTitleFxn}"} onClick.content={sequenceTitleFxn} diff --git a/Model/lib/jbrowse/hcapG217B/tracks.conf b/Model/lib/jbrowse/hcapG217B/tracks.conf index 312ca1265..928e42c6d 100644 --- a/Model/lib/jbrowse/hcapG217B/tracks.conf +++ b/Model/lib/jbrowse/hcapG217B/tracks.conf @@ -1,19 +1,16 @@ [tracks.hcapG217B_bld63Transcripts_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='hcapG217B_bld63Transcripts_transcript_sequences_RSRC' category=Gene Models -key=Histoplasma capsulatum G217B transcripts from build 63 models -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +key=Histoplasma capsulatum G217B transcripts from build 63 models +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=HcapsulatumG217B/alignedTranscripts/gff/hcapG217B_bld63Transcripts_transcript_sequences_RSRC/hcapG217B_bld63Transcripts_transcript_sequences_RSRC.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript style.utrColor=grey style.color={alternateTranscriptColor} metadata.subcategory=Transcripts metadata.trackType=Processed Transcript -metadata.dataset=Histoplasma capsulatum G217B transcripts from build 63 models -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("hcapG217B_bld63Transcripts_transcript_sequences_RSRC", "Histoplasma capsulatum G217B transcripts from build 63 models"); } +metadata.dataset=Histoplasma capsulatum G217B transcripts from build 63 models +fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("hcapG217B_bld63Transcripts_transcript_sequences_RSRC", "Histoplasma capsulatum G217B transcripts from build 63 models"); } menuTemplate+=json:{"label": "View Details", "content": "{sequenceTitleFxn}"} onClick.content={sequenceTitleFxn} diff --git a/Model/lib/jbrowse/hcapH88/tracks.conf b/Model/lib/jbrowse/hcapH88/tracks.conf index b6359e504..6ff546345 100644 --- a/Model/lib/jbrowse/hcapH88/tracks.conf +++ b/Model/lib/jbrowse/hcapH88/tracks.conf @@ -1,19 +1,16 @@ [tracks.hcapH88_bld63Transcripts_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='hcapH88_bld63Transcripts_transcript_sequences_RSRC' category=Gene Models -key=Histoplasma capsulatum H88 transcripts from build 63 models -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +key=Histoplasma capsulatum H88 transcripts from build 63 models +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=HcapsulatumH88/alignedTranscripts/gff/hcapH88_bld63Transcripts_transcript_sequences_RSRC/hcapH88_bld63Transcripts_transcript_sequences_RSRC.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript style.utrColor=grey style.color={alternateTranscriptColor} metadata.subcategory=Transcripts metadata.trackType=Processed Transcript -metadata.dataset=Histoplasma capsulatum H88 transcripts from build 63 models -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("hcapH88_bld63Transcripts_transcript_sequences_RSRC", "Histoplasma capsulatum H88 transcripts from build 63 models"); } +metadata.dataset=Histoplasma capsulatum H88 transcripts from build 63 models +fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("hcapH88_bld63Transcripts_transcript_sequences_RSRC", "Histoplasma capsulatum H88 transcripts from build 63 models"); } menuTemplate+=json:{"label": "View Details", "content": "{sequenceTitleFxn}"} onClick.content={sequenceTitleFxn} diff --git a/Model/lib/jbrowse/iscaPalLabHiFi/tracks.conf b/Model/lib/jbrowse/iscaPalLabHiFi/tracks.conf index af592ee85..a24942a5b 100644 --- a/Model/lib/jbrowse/iscaPalLabHiFi/tracks.conf +++ b/Model/lib/jbrowse/iscaPalLabHiFi/tracks.conf @@ -1,14 +1,19 @@ [tracks.iscaPalLabHiFi_WickelAnnotation2Palhifi_GFF_RSRC] -query.feature=gff:processedTranscript -query.edName='iscaPalLabHiFi_WickelAnnotation2Palhifi_GFF_RSRC' category=Gene Models key=Gene models of I. scapularis Wickel -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/CanvasFeatures -glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript -style.utrColor=grey +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=IscapularisPalLabHiFi/prealigned/gff/iscaPalLabHiFi_WickelAnnotation2Palhifi_WebService_RSRC/iscaPalLabHiFi_WickelAnnotation2Palhifi.gff.gz +type=NeatCanvasFeatures/View/Track/NeatFeatures +glyph=NeatCanvasFeatures/View/FeatureGlyph/Gene +transcriptType={geneTranscriptType} +noncodingType=nc_transcript +labelTranscripts=false +unsafePopup="JSON::true" style.color={alternateTranscriptColor} +style.borderColor={processedTranscriptBorderColor} +style.utrColor=grey +style.topLevelFeaturesPercent=10 +style.labelScale=0.01 onClick.content={gffGeneFeatureTitleFxn} menuTemplate+=json:{"label": "View Details", "content": "{gffGeneFeatureTitleFxn}"} metadata.subcategory=Transcripts diff --git a/Model/lib/jbrowse/lbraMHOMBR75M2904_2019/tracks.conf b/Model/lib/jbrowse/lbraMHOMBR75M2904_2019/tracks.conf index 7eaeee3e9..3111f4ba8 100644 --- a/Model/lib/jbrowse/lbraMHOMBR75M2904_2019/tracks.conf +++ b/Model/lib/jbrowse/lbraMHOMBR75M2904_2019/tracks.conf @@ -1,13 +1,10 @@ lbraMHOMBR75M2904_2019_maxicircle_gene_model_transcript_sequences_RSRC [tracks.lbraMHOMBR75M2904_2019_maxicircle_gene_model_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='lbraMHOMBR75M2904_2019_maxicircle_gene_model_transcript_sequences_RSRC' category=Gene Models key=Maxicircle Annotation -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=LbraziliensisMHOMBR75M2904_2019/alignedTranscripts/gff/lbraMHOMBR75M2904_2019_maxicircle_gene_model_transcript_sequences_RSRC/lbraMHOMBR75M2904_2019_maxicircle_gene_model_transcript_sequences_RSRC.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript style.utrColor=grey diff --git a/Model/lib/jbrowse/ldonLV9/tracks.conf b/Model/lib/jbrowse/ldonLV9/tracks.conf index 21953f209..f9b8afeb4 100644 --- a/Model/lib/jbrowse/ldonLV9/tracks.conf +++ b/Model/lib/jbrowse/ldonLV9/tracks.conf @@ -1,11 +1,8 @@ [tracks.ldonLV9_maxicircle_gene_model_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='ldonLV9_maxicircle_gene_model_transcript_sequences_RSRC' category=Gene Models key=Maxicircle Annotation -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=LdonovaniLV9/alignedTranscripts/gff/ldonLV9_maxicircle_gene_model_transcript_sequences_RSRC/ldonLV9_maxicircle_gene_model_transcript_sequences_RSRC.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript style.utrColor=grey diff --git a/Model/lib/jbrowse/llonM1/tracks.conf b/Model/lib/jbrowse/llonM1/tracks.conf index 633597690..6da6ca2bc 100644 --- a/Model/lib/jbrowse/llonM1/tracks.conf +++ b/Model/lib/jbrowse/llonM1/tracks.conf @@ -1,19 +1,22 @@ [tracks.llonM1_LlonJ16_liftoff_phase_corrected_GFF_RSRC] -query.feature=gff:processedTranscript -query.edName='llonM1_LlonJ1.6_liftoff_phase_corrected_GFF_RSRC' category=Gene Models metadata.subcategory=Transcripts metadata.trackType=Processed Transcript -storeClass=JBrowse/Store/SeqFeature/REST +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=LlongipalpisM1/prealigned/gff/llonM1_LlonJ1.6_liftoff_phase_corrected_WebService_RSRC/llonM1_LlonJ1.6_liftoff_phase_corrected.gff.gz +type=NeatCanvasFeatures/View/Track/NeatFeatures +glyph=NeatCanvasFeatures/View/FeatureGlyph/Gene +transcriptType={geneTranscriptType} +noncodingType=nc_transcript +labelTranscripts=false +unsafePopup="JSON::true" style.color={liftoffTranscriptColor} style.borderColor={processedTranscriptBorderColor} style.utrColor=grey -baseUrl=/a/service/jbrowse -#glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript -type=NeatCanvasFeatures/View/Track/NeatFeatures +style.topLevelFeaturesPercent=10 +style.labelScale=0.01 key=Liftoff Gene models of LlonJ1.6 to llonM1 -unsafePopup="JSON::true" onClick.content={liftoffGeneDetails} metadata.dataset= fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("llonM1_LlonJ1.6_liftoff_phase_corrected_GFF_RSRC", "Liftoff Gene models of LlonJ1.6 to llonM1"); } diff --git a/Model/lib/jbrowse/mcirCBS277-49/tracks.conf b/Model/lib/jbrowse/mcirCBS277-49/tracks.conf index 04c4e42e5..f7eff0034 100644 --- a/Model/lib/jbrowse/mcirCBS277-49/tracks.conf +++ b/Model/lib/jbrowse/mcirCBS277-49/tracks.conf @@ -1,18 +1,16 @@ [tracks.mcirCBS277-49_bld60Transcripts_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='mcirCBS277-49_bld60Transcripts_transcript_sequences_RSRC' category=Gene Models key=Mucor lusitanicus CBS 277.49 previous annotation track -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=MlusitanicusCBS277-49/alignedTranscripts/gff/mcirCBS277-49_bld60Transcripts_transcript_sequences_RSRC/mcirCBS277-49_bld60Transcripts_transcript_sequences_RSRC.gff.gz +subParts=veupathdb type=JBrowse/View/Track/CanvasFeatures -glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript -style.utrColor=grey +glyph=JBrowse/View/FeatureGlyph/Segments style.color={alternateTranscriptColor} +style.label=function(feature){ return feature.get("transcriptid"); } metadata.subcategory=Transcripts metadata.trackType=Processed Transcript metadata.dataset=Mucor lusitanicus CBS 277.49 previous annotation track fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("mcirCBS277-49_bld60Transcripts_transcript_sequences_RSRC", "Mucor lusitanicus CBS 277.49 previous annotation track"); } menuTemplate+=json:{"label": "View Details", "content": "{sequenceTitleFxn}"} -onClick.content={sequenceTitleFxn} +onClick.content=function(track, feature){ var c = track.browser.config; return c.sequenceTitleFxn(track, feature) } diff --git a/Model/lib/jbrowse/pcapLT15342021/tracks.conf b/Model/lib/jbrowse/pcapLT15342021/tracks.conf index 900524165..cf8b0f173 100644 --- a/Model/lib/jbrowse/pcapLT15342021/tracks.conf +++ b/Model/lib/jbrowse/pcapLT15342021/tracks.conf @@ -1,19 +1,17 @@ [tracks.pcapLT15342021_GCA_000325885.1Transcripts_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='pcapLT15342021_GCA_000325885.1Transcripts_transcript_sequences_RSRC' category=Gene Models key=Transcript alignment from JCVI annotation -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=PcapsiciLT1534/alignedTranscripts/gff/pcapLT1534_GCA_000325885.1Transcripts_transcript_sequences_RSRC/pcapLT1534_GCA_000325885.1Transcripts_transcript_sequences_RSRC.gff.gz +subParts=veupathdb type=JBrowse/View/Track/CanvasFeatures -glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript -style.utrColor=grey +glyph=JBrowse/View/FeatureGlyph/Segments style.color={alternateTranscriptColor} +style.label=function(feature){ return feature.get("transcriptid"); } metadata.subcategory=Transcripts metadata.trackType=Processed Transcript metadata.dataset=Transcript alignment from JCVI annotation fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("pcapLT15342021_GCA_000325885.1Transcripts_transcript_sequences_RSRC", "Transcript alignment from JCVI annotation"); } menuTemplate+=json:{"label": "View Details", "content": "{sequenceTitleFxn}"} -onClick.content={sequenceTitleFxn} +onClick.content=function(track, feature){ var c = track.browser.config; return c.sequenceTitleFxn(track, feature) } diff --git a/Model/lib/jbrowse/ppapM1/tracks.conf b/Model/lib/jbrowse/ppapM1/tracks.conf index 50f2f35ac..65a883cb7 100644 --- a/Model/lib/jbrowse/ppapM1/tracks.conf +++ b/Model/lib/jbrowse/ppapM1/tracks.conf @@ -1,19 +1,22 @@ [tracks.ppapM1_PpapI16_liftoff_phase_corrected_GFF_RSRC] -query.feature=gff:processedTranscript -query.edName='ppapM1_PpapI1.6_liftoff_phase_corrected_GFF_RSRC' category=Gene Models metadata.subcategory=Transcripts metadata.trackType=Processed Transcript -storeClass=JBrowse/Store/SeqFeature/REST +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=PpapatasiM1/prealigned/gff/ppapM1_PpapI1.6_liftoff_phase_corrected_WebService_RSRC/ppapM1_PpapI1.6_liftoff_phase_corrected.gff.gz +type=NeatCanvasFeatures/View/Track/NeatFeatures +glyph=NeatCanvasFeatures/View/FeatureGlyph/Gene +transcriptType={geneTranscriptType} +noncodingType=nc_transcript +labelTranscripts=false +unsafePopup="JSON::true" style.color={liftoffTranscriptColor} style.borderColor={processedTranscriptBorderColor} style.utrColor=grey -baseUrl=/a/service/jbrowse -#glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript -type=NeatCanvasFeatures/View/Track/NeatFeatures +style.topLevelFeaturesPercent=10 +style.labelScale=0.01 key=Liftoff Gene models of PpapI1.6 to ppapM1 -unsafePopup="JSON::true" onClick.content={liftoffGeneDetails} metadata.dataset= fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("ppapM1_PpapI1.6_liftoff_phase_corrected_GFF_RSRC", "Liftoff Gene models of PpapI1.6 to ppapM1"); } diff --git a/Model/lib/jbrowse/rproCDC/tracks.conf b/Model/lib/jbrowse/rproCDC/tracks.conf index 677438161..3cb1759fd 100644 --- a/Model/lib/jbrowse/rproCDC/tracks.conf +++ b/Model/lib/jbrowse/rproCDC/tracks.conf @@ -1,11 +1,8 @@ [tracks.rproCDC_bld54Transcripts_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='rproCDC_bld54Transcripts_transcript_sequences_RSRC' category=Gene Models key=Rhodnius prolixus CDC build 54 models -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=RprolixusCDC/alignedTranscripts/gff/rproCDC_bld54Transcripts_transcript_sequences_RSRC/rproCDC_bld54Transcripts_transcript_sequences_RSRC.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript style.utrColor=grey diff --git a/Model/lib/jbrowse/ssalATCC50377/tracks.conf b/Model/lib/jbrowse/ssalATCC50377/tracks.conf index c872f3b9b..6ac99ff7d 100644 --- a/Model/lib/jbrowse/ssalATCC50377/tracks.conf +++ b/Model/lib/jbrowse/ssalATCC50377/tracks.conf @@ -1,11 +1,8 @@ [tracks.ssalATCC50377_bld60Transcripts_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='ssalATCC50377_bld60Transcripts_transcript_sequences_RSRC' category=Gene Models key=S. salmonicida ATCC50377 transcripts from Release 60 -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=SsalmonicidaATCC50377/alignedTranscripts/gff/ssalATCC50377_bld60Transcripts_transcript_sequences_RSRC/ssalATCC50377_bld60Transcripts_transcript_sequences_RSRC.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript style.utrColor=grey diff --git a/Model/lib/jbrowse/ssch1099-18/tracks.conf b/Model/lib/jbrowse/ssch1099-18/tracks.conf index 6099a15a3..417d56bd5 100644 --- a/Model/lib/jbrowse/ssch1099-18/tracks.conf +++ b/Model/lib/jbrowse/ssch1099-18/tracks.conf @@ -1,17 +1,12 @@ [tracks.ssch1099-18_Romeo_MYA-4821_2020-manual] -query.feature=gff:basicAlt -query.edName='ssch1099-18_Romeo_MYA-4821_2020_annotation_GFF_RSRC' -query.source='manual' category=Gene Models -storeClass=JBrowse/Store/SeqFeature/REST +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=Sschenckii1099-18/prealigned/gff/ssch1099-18_Romeo_MYA-4821_2020_annotation_WebService_RSRC/ssch1099-18_Romeo_MYA-4821_2020_annotation.gff.gz style.color={processedGffColor} -baseUrl=/a/service/jbrowse type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/Box style.strandArrow=false key=Sporothrix schenckii 1099-18 (ATCC MYA-4821) re-annotation (manual) (Giosa et al. 2020) -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/CanvasFeatures displayMode=normal metadata.subcategory=Transcripts metadata.trackType=Segments @@ -22,19 +17,14 @@ fmtMetaValue_Description=function() { return datasetDescription("S. schenckii st [tracks.ssch1099-18_Romeo_MYA-4821_2020-maker] -query.feature=gff:basicAlt -query.edName='ssch1099-18_Romeo_MYA-4821_2020_annotation_GFF_RSRC' -query.source='maker' category=Gene Models -storeClass=JBrowse/Store/SeqFeature/REST +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=Sschenckii1099-18/prealigned/gff/ssch1099-18_Romeo_MYA-4821_2020_annotation_WebService_RSRC/ssch1099-18_Romeo_MYA-4821_2020_annotation.gff.gz style.color={processedGffColor} -baseUrl=/a/service/jbrowse type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/Box style.strandArrow=false key=Sporothrix schenckii 1099-18 (ATCC MYA-4821) re-annotation (Maker) (Giosa et al. 2020) -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/CanvasFeatures displayMode=normal metadata.subcategory=Transcripts metadata.trackType=Segments diff --git a/Model/lib/jbrowse/tcruBrazilA4/tracks.conf b/Model/lib/jbrowse/tcruBrazilA4/tracks.conf index 41523b050..f98cfd7a9 100644 --- a/Model/lib/jbrowse/tcruBrazilA4/tracks.conf +++ b/Model/lib/jbrowse/tcruBrazilA4/tracks.conf @@ -1,6 +1,6 @@ [tracks.tcruBrazilA4_Robello_genomeCompartment_RSRC_core] storeClass=JBrowse/Store/SeqFeature/BigWig -urlTemplate=/a/service/jbrowse/store?data=TcruziBrazilA4/bigwig/tcruBrazilA4_Robello_genomeCompartment_RSRC/BrazilA4_core_compartment_positions.bw +urlTemplate=/a/service/jbrowse/store?data=TcruziBrazilA4/prealigned/bigwig/tcruBrazilA4_Robello_genomeCompartment_WebService_RSRC/BrazilA4_core_compartment_positions.bw key=Core genome compartments in T cruzi Brazil A4 label=Core genome compartments in T cruzi Brazil A4 category=Gene Models @@ -18,7 +18,7 @@ yScalePosition=left [tracks.tcruBrazilA4_Robello_genomeCompartment_RSRC_disruptive] storeClass=JBrowse/Store/SeqFeature/BigWig -urlTemplate=/a/service/jbrowse/store?data=TcruziBrazilA4/bigwig/tcruBrazilA4_Robello_genomeCompartment_RSRC/BrazilA4_disruptive_compartment_positions.bw +urlTemplate=/a/service/jbrowse/store?data=TcruziBrazilA4/prealigned/bigwig/tcruBrazilA4_Robello_genomeCompartment_WebService_RSRC/BrazilA4_disruptive_compartment_positions.bw key=Disruptive) genome compartments in T cruzi Brazil A4 label=Disruptive) genome compartments in T cruzi Brazil A4 category=Gene Models diff --git a/Model/lib/jbrowse/tcruCLBrenerEsmeraldo-like/tracks.conf b/Model/lib/jbrowse/tcruCLBrenerEsmeraldo-like/tracks.conf index 4dfc60da3..ead066d36 100644 --- a/Model/lib/jbrowse/tcruCLBrenerEsmeraldo-like/tracks.conf +++ b/Model/lib/jbrowse/tcruCLBrenerEsmeraldo-like/tracks.conf @@ -16,663 +16,3 @@ onClick.content=function(track, feature){ var c = track.browser.config; return c menuTemplate+=json:{"label": "View Details", "content": "function(track, feature){ var c = track.browser.config; return c.arrayElementTitle(track, feature, 'Expression')}"} region_feature_densities=true #citation = Trypanosoma cruzi Oligonucleotide Array v1; Manufacturer = PFGRC; Contact: Todd Minning, tminning@uga.edu; (For details: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL8132) - -[tracks.Cnv10R26] -query.feature=cnv:ArrayJBrowse -query.sample=10R26 (CGH Array) -category=Genetic Variation -key=10R26 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=10R26 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.Cnv92_80] -query.feature=cnv:ArrayJBrowse -query.sample=92.80 (CGH Array) -category=Genetic Variation -key=92.80 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=92.80 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.Cnv9210160P] -query.feature=cnv:ArrayJBrowse -query.sample=9210160P (CGH Array) -category=Genetic Variation -key=9210160P (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=9210160P (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvARMA18] -query.feature=cnv:ArrayJBrowse -query.sample=ARMA18 (CGH Array) -category=Genetic Variation -key=ARMA18 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=ARMA18 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvBrazil] -query.feature=cnv:ArrayJBrowse -query.sample=Brazil (CGH Array) -category=Genetic Variation -key=Brazil (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=Brazil (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvBug2148] -query.feature=cnv:ArrayJBrowse -query.sample=Bug2148 (CGH Array) -category=Genetic Variation -key=Bug2148 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=Bug2148 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvCBB] -query.feature=cnv:ArrayJBrowse -query.sample=CBB (CGH Array) -category=Genetic Variation -key=CBB (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=CBB (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvCL] -query.feature=cnv:ArrayJBrowse -query.sample=CL (CGH Array) -category=Genetic Variation -key=CL (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=CL (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvCanIII] -query.feature=cnv:ArrayJBrowse -query.sample=CanIII (CGH Array) -category=Genetic Variation -key=CanIII (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=CanIII (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvChaco23] -query.feature=cnv:ArrayJBrowse -query.sample=Chaco23 (CGH Array) -category=Genetic Variation -key=Chaco23 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=Chaco23 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvChaco9] -query.feature=cnv:ArrayJBrowse -query.sample=Chaco9 (CGH Array) -category=Genetic Variation -key=Chaco9 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=Chaco9 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvChinata] -query.feature=cnv:ArrayJBrowse -query.sample=Chinata (CGH Array) -category=Genetic Variation -key=Chinata (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=Chinata (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvColombiana] -query.feature=cnv:ArrayJBrowse -query.sample=Colombiana (CGH Array) -category=Genetic Variation -key=Colombiana (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=Colombiana (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvEPV20] -query.feature=cnv:ArrayJBrowse -query.sample=EPV20 (CGH Array) -category=Genetic Variation -key=EPV20 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=EPV20 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvEsmeraldo] -query.feature=cnv:ArrayJBrowse -query.sample=Esmeraldo (CGH Array) -category=Genetic Variation -key=Esmeraldo (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=Esmeraldo (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvG] -query.feature=cnv:ArrayJBrowse -query.sample=G (CGH Array) -category=Genetic Variation -key=G (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=G (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvM5631] -query.feature=cnv:ArrayJBrowse -query.sample=M5631 (CGH Array) -category=Genetic Variation -key=M5631 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=M5631 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvM6421] -query.feature=cnv:ArrayJBrowse -query.sample=M6421 (CGH Array) -category=Genetic Variation -key=M6421 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=M6421 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvM78] -query.feature=cnv:ArrayJBrowse -query.sample=M78 (CGH Array) -category=Genetic Variation -key=M78 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=M78 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvMontalvania] -query.feature=cnv:ArrayJBrowse -query.sample=Montalvania (CGH Array) -category=Genetic Variation -key=Montalvania (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=Montalvania (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvP251] -query.feature=cnv:ArrayJBrowse -query.sample=P251 (CGH Array) -category=Genetic Variation -key=P251 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=P251 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvPalDa_cl9] -query.feature=cnv:ArrayJBrowse -query.sample=PalDa_cl9 (CGH Array) -category=Genetic Variation -key=PalDa_cl9 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=PalDa_cl9 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvPara4] -query.feature=cnv:ArrayJBrowse -query.sample=Para4 (CGH Array) -category=Genetic Variation -key=Para4 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=Para4 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvSABP19] -query.feature=cnv:ArrayJBrowse -query.sample=SABP19 (CGH Array) -category=Genetic Variation -key=SABP19 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=SABP19 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvStC10R] -query.feature=cnv:ArrayJBrowse -query.sample=StC10R (CGH Array) -category=Genetic Variation -key=StC10R (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=StC10R (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvSylvio_X10] -query.feature=cnv:ArrayJBrowse -query.sample=Sylvio_X10 (CGH Array) -category=Genetic Variation -key=Sylvio_X10 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=Sylvio_X10 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvTCC] -query.feature=cnv:ArrayJBrowse -query.sample=TCC (CGH Array) -category=Genetic Variation -key=TCC (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=TCC (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvTEDa2_cl4] -query.feature=cnv:ArrayJBrowse -query.sample=TEDa2_cl4 (CGH Array) -category=Genetic Variation -key=TEDa2_cl4 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=TEDa2_cl4 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvTEP6_cl5] -query.feature=cnv:ArrayJBrowse -query.sample=TEP6_cl5 (CGH Array) -category=Genetic Variation -key=TEP6_cl5 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=TEP6_cl5 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvTu18] -query.feature=cnv:ArrayJBrowse -query.sample=Tu18 (CGH Array) -category=Genetic Variation -key=Tu18 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=Tu18 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvTu18_cl1] -query.feature=cnv:ArrayJBrowse -query.sample=Tu18_cl1 (CGH Array) -category=Genetic Variation -key=Tu18_cl1 (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=Tu18_cl1 (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvTulahuen] -query.feature=cnv:ArrayJBrowse -query.sample=Tulahuen (CGH Array) -category=Genetic Variation -key=Tulahuen (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=Tulahuen (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } - -[tracks.CnvY] -query.feature=cnv:ArrayJBrowse -query.sample=Y (CGH Array) -category=Genetic Variation -key=Y (CGH Array) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/Wiggle/XYPlot -metadata.subcategory=CGH Array -metadata.trackType=XYPlot -metadata.dataset=Comparative Genomic Hybridizations of 33 strains -metadata.description=Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization -style.height=40 -yScalePosition=left -max_score=3 -label=Y (CGH Array) -min_score=-3 -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName('tcruCLBrenerEsmeraldo-like_cghArrayPlatform_GPL10781_RSRC', 'Comparative Genomic Hybridizations of 33 strains'); } -fmtMetaValue_Description=function() { return datasetDescription('Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization ', ''); } diff --git a/Model/lib/jbrowse/tgonGT1/tracks.conf b/Model/lib/jbrowse/tgonGT1/tracks.conf index a1b8a7774..03cf9026b 100644 --- a/Model/lib/jbrowse/tgonGT1/tracks.conf +++ b/Model/lib/jbrowse/tgonGT1/tracks.conf @@ -1,15 +1,13 @@ [tracks.CrisprPhenotypeGuideRNA] -query.feature=gff:basic -query.edName='tgonGT1_CrisprScreen_GFF_topLevel_RSRC' category=Sequence Analysis metadata.subcategory=Sequence sites, features and motifs key=CRISPR Screen gRNAs -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=TgondiiGT1/prealigned/gff/tgonGT1_CrisprScreen_WebService_RSRC/tgonGT1_CrisprScreen.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/Box metadata.dataset=Fitness during the T. gondii lytic cycle. (Genome-Wide CRISPR Screen) -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("tgonGT1_CrisprScreen_GFF_topLevel_RSRC", "Fitness during the T. gondii lytic cycle. (Genome-Wide CRISPR Screen)"); } +fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName(" tgonGT1_CrisprScreen_WebService_RSRC", "Fitness during the T. gondii lytic cycle. (Genome-Wide CRISPR Screen)"); } style.color=black style.strandArrow=false metadata.trackType=Segments diff --git a/Model/lib/jbrowse/tgonME49/tracks.conf b/Model/lib/jbrowse/tgonME49/tracks.conf index 08532748c..5f7a67e21 100644 --- a/Model/lib/jbrowse/tgonME49/tracks.conf +++ b/Model/lib/jbrowse/tgonME49/tracks.conf @@ -270,97 +270,128 @@ style.neg_color=red style.height=40 [tracks.denovo_union] -query.feature=gff:processedTranscript -query.edName='tgonME49_me49.denovo.craig_GFF_topLevel_RSRC' category=Gene Models key=CRAIG denovo Gene Model Prediction -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/CanvasFeatures -glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript -style.utrColor=grey +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=TgondiiME49/prealigned/gff/tgonME49_me49.denovo.craig_WebService_RSRC/tgonME49_me49.denovo.craig.gff.gz +type=NeatCanvasFeatures/View/Track/NeatFeatures +glyph=NeatCanvasFeatures/View/FeatureGlyph/Gene +transcriptType={geneTranscriptType} +noncodingType=nc_transcript +labelTranscripts=false +unsafePopup="JSON::true" style.color={alternateTranscriptColor} +style.borderColor={processedTranscriptBorderColor} +style.utrColor=grey +style.topLevelFeaturesPercent=10 +style.labelScale=0.01 onClick.content={gffGeneFeatureTitleFxn} menuTemplate+=json:{"label": "View Details", "content": "{gffGeneFeatureTitleFxn}"} metadata.subcategory=Transcripts metadata.trackType=Processed Transcript [tracks.utr_only_union] -query.feature=gff:processedTranscript -query.edName='tgonME49_unionized_cds_GFF_topLevel_RSRC' category=Gene Models key=Annotated Transcripts w/ CRAIG UTR Prediction -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/CanvasFeatures -glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript -style.utrColor=grey +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=TgondiiME49/prealigned/gff/tgonME49_unionized_cds_WebService_RSRC/tgonME49_unionized_cds.gff.gz +type=NeatCanvasFeatures/View/Track/NeatFeatures +glyph=NeatCanvasFeatures/View/FeatureGlyph/Gene +transcriptType={geneTranscriptType} +noncodingType=nc_transcript +labelTranscripts=false +unsafePopup="JSON::true" style.color={alternateTranscriptColor} +style.borderColor={processedTranscriptBorderColor} +style.utrColor=grey +style.topLevelFeaturesPercent=10 +style.labelScale=0.01 onClick.content={gffGeneFeatureTitleFxn} menuTemplate+=json:{"label": "View Details", "content": "{gffGeneFeatureTitleFxn}"} metadata.subcategory=Transcripts metadata.trackType=Processed Transcript [tracks.utr_only_scores] -query.feature=gff:processedTranscript -query.edName='tgonME49_predictions_utr_scores_GFF_topLevel_RSRC' category=Gene Models key=Annotated Transcripts w/ CRAIG UTR Prediction (highest score) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/CanvasFeatures -glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript -style.utrColor=grey +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=TgondiiME49/prealigned/gff/tgonME49_predictions_utr_scores_WebService_RSRC/tgonME49_predictions_utr_scores.gff.gz +type=NeatCanvasFeatures/View/Track/NeatFeatures +glyph=NeatCanvasFeatures/View/FeatureGlyph/Gene +transcriptType={geneTranscriptType} +noncodingType=nc_transcript +labelTranscripts=false +unsafePopup="JSON::true" style.color={alternateTranscriptColor} +style.borderColor={processedTranscriptBorderColor} +style.utrColor=grey +style.topLevelFeaturesPercent=10 +style.labelScale=0.01 onClick.content={gffGeneFeatureTitleFxn} menuTemplate+=json:{"label": "View Details", "content": "{gffGeneFeatureTitleFxn}"} metadata.subcategory=Transcripts metadata.trackType=Processed Transcript [tracks.utr_only_lengths] -query.feature=gff:processedTranscript -query.edName='tgonME49_predictions_utr_lengths_GFF_topLevel_RSRC' category=Gene Models key=Annotated Transcripts w/ CRAIG UTR Prediction (longest) -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/CanvasFeatures -glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript -style.utrColor=grey +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=TgondiiME49/prealigned/gff/tgonME49_predictions_utr_lengths_WebService_RSRC/tgonME49_predictions_utr_lengths.gff.gz +type=NeatCanvasFeatures/View/Track/NeatFeatures +glyph=NeatCanvasFeatures/View/FeatureGlyph/Gene +transcriptType={geneTranscriptType} +noncodingType=nc_transcript +labelTranscripts=false +unsafePopup="JSON::true" style.color={alternateTranscriptColor} +style.borderColor={processedTranscriptBorderColor} +style.utrColor=grey +style.topLevelFeaturesPercent=10 +style.labelScale=0.01 onClick.content={gffGeneFeatureTitleFxn} menuTemplate+=json:{"label": "View Details", "content": "{gffGeneFeatureTitleFxn}"} metadata.subcategory=Transcripts metadata.trackType=Processed Transcript [tracks.craig12SamplesUtrOnly] -query.feature=gff:processedTranscript -query.edName='tgonME49_craig_UTR_GFF_topLevel_RSRC' category=Gene Models key=Annotated Transcripts w/ CRAIG UTR Predictions from 12 samples -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/CanvasFeatures -glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript -style.utrColor=grey +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=TgondiiME49/prealigned/gff/tgonME49_craig_UTR_WebService_RSRC/tgonME49_craig_UTR.gff.gz +type=NeatCanvasFeatures/View/Track/NeatFeatures +glyph=NeatCanvasFeatures/View/FeatureGlyph/Gene +transcriptType={geneTranscriptType} +noncodingType=nc_transcript +labelTranscripts=false +unsafePopup="JSON::true" style.color={alternateTranscriptColor} +style.borderColor={processedTranscriptBorderColor} +style.utrColor=grey +style.topLevelFeaturesPercent=10 +style.labelScale=0.01 onClick.content={gffGeneFeatureTitleFxn} menuTemplate+=json:{"label": "View Details", "content": "{gffGeneFeatureTitleFxn}"} metadata.subcategory=Transcripts metadata.trackType=Processed Transcript [tracks.craig12SamplesDeNovo] -query.feature=gff:processedTranscript -query.edName='tgonME49_craig_denovo_GFF_topLevel_RSRC' category=Gene Models key=CRAIG De Novo Predictions from 12 samples -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/CanvasFeatures -glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript -style.utrColor=grey +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=TgondiiME49/prealigned/gff/tgonME49_craig_denovo_WebService_RSRC/tgonME49_craig_denovo.gff.gz +type=NeatCanvasFeatures/View/Track/NeatFeatures +glyph=NeatCanvasFeatures/View/FeatureGlyph/Gene +transcriptType={geneTranscriptType} +noncodingType=nc_transcript +labelTranscripts=false +unsafePopup="JSON::true" style.color={alternateTranscriptColor} +style.borderColor={processedTranscriptBorderColor} +style.utrColor=grey +style.topLevelFeaturesPercent=10 +style.labelScale=0.01 onClick.content={gffGeneFeatureTitleFxn} +menuTemplate+=json:{"label": "View Details", "content": "{gffGeneFeatureTitleFxn}"} metadata.subcategory=Transcripts metadata.trackType=Processed Transcript @@ -577,63 +608,65 @@ region_feature_densities=true [tracks.tgonME49_bld73Transcripts_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='tgonME49_bld7.3Transcripts_transcript_sequences_RSRC' category=Gene Models key=ToxoDB7.3 Transcripts -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=TgondiiME49/alignedTranscripts/gff/tgonME49_bld7.3Transcripts_transcript_sequences_RSRC/tgonME49_bld7.3Transcripts_transcript_sequences_RSRC.gff.gz +subParts=veupathdb type=JBrowse/View/Track/CanvasFeatures -glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript -style.utrColor=grey +glyph=JBrowse/View/FeatureGlyph/Segments style.color={alternateTranscriptColor} +style.label=function(feature){ return feature.get("transcriptid"); } metadata.subcategory=Transcripts metadata.trackType=Processed Transcript metadata.dataset=ToxoDB7.3 Transcripts fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("tgonME49_bld7.3Transcripts_transcript_sequences_RSRC", "ToxoDB7.3 Transcripts"); } +onClick.content=function(track, feature){ var c = track.browser.config; return c.sequenceTitleFxn(track, feature) } menuTemplate+=json:{"label": "View Details", "content": "{sequenceTitleFxn}"} -onClick.content={sequenceTitleFxn} [tracks.tgonME49_bld65Annotation_GFF_topLevel_RSRC] -query.feature=gff:processedTranscript -query.edName='tgonME49_bld65Annotation_GFF_topLevel_RSRC' category=Gene Models key=T.gondii ME49 transcripts from Release 65 -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/CanvasFeatures -glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript -style.utrColor=grey +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=TgondiiME49/prealigned/gff/tgonME49_bld65Annotation_WebService_RSRC/tgonME49_bld65Annotation.gff.gz +type=NeatCanvasFeatures/View/Track/NeatFeatures +glyph=NeatCanvasFeatures/View/FeatureGlyph/Gene +transcriptType={geneTranscriptType} +noncodingType=nc_transcript +labelTranscripts=false +unsafePopup="JSON::true" style.color={alternateTranscriptColor} -onClick.content={gffGeneFeatureTitleFxn} +style.borderColor={processedTranscriptBorderColor} +style.utrColor=grey +style.topLevelFeaturesPercent=10 +style.labelScale=0.01 +onClick.content=function(track, feature){ var c = track.browser.config; return c.gffGeneFeatureTitleFxn(track,feature) } metadata.subcategory=Transcripts metadata.trackType=Processed Transcript [tracks.tgonME49_Sullivan_m6A_GFF_RSRC] -query.feature=gff:basic -query.edName='tgonME49_Sullivan_m6A_GFF_RSRC' category=Epigenomics metadata.subcategory=Sequence sites, features and motifs key=Epitranscriptome of m6A -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=TgondiiME49/prealigned/gff/tgonME49_Sullivan_m6A_WebService_RSRC/tgonME49_Sullivan_m6A.gff.gz type=EbrcTracks/View/Track/CanvasSubtracks glyph=JBrowse/View/FeatureGlyph/Box metadata.trackType=Segments -style.color={gffColorFxn} +style.color=function(feature){ var dbToColor = {'m6A_combined':'grey','m6A_after_24h_alkaline_stress':'purple','m6A_in_tachyzoites':'green'}; return dbToColor[feature.get("source")] || 'grey'; } style.strandArrow=false style.showLabels=false -onClick.content={gffTitleFxn} +unsafePopup="JSON::true" +onClick.content=function(track, feature){ var c = track.browser.config; return c.gffTitle(track, feature) } menuTemplate+=json:{"label": "View Details", "content": "{gffTitleFxn}"} metadata.description=m6A: m6A combined, m6A after 24h alkaline stress, m6A in tachyzoites -subtracks+=json:{"featureFilters":{"source":"m6A combined"},"visible":1,"label":"m6A combined","metadata":{}} -subtracks+=json:{"featureFilters":{"source":"m6A after 24h alkaline stress"},"visible":1,"label":"m6A after 24h alkaline stress","metadata":{}} -subtracks+=json:{"featureFilters":{"source":"m6A in tachyzoites"},"visible":1,"label":"m6A in tachyzoites","metadata":{}} +subtracks+=json:{"featureFilters":{"source":"m6A_combined"},"visible":1,"label":"m6A combined","metadata":{}} +subtracks+=json:{"featureFilters":{"source":"m6A_after_24h_alkaline_stress"},"visible":1,"label":"m6A after 24h alkaline stress","metadata":{}} +subtracks+=json:{"featureFilters":{"source":"m6A_in_tachyzoites"},"visible":1,"label":"m6A in tachyzoites","metadata":{}} metadata.dataset=Epitranscriptome of m6A -fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("tgonME49_Sullivan_m6A_GFF_RSRC", "Epitranscriptome of m6A"); } +fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("tgonME49_Sullivan_m6A_WebService_RSRC", "Epitranscriptome of m6A"); } diff --git a/Model/lib/jbrowse/treeQM6a/tracks.conf b/Model/lib/jbrowse/treeQM6a/tracks.conf index 39cd309ac..611c613de 100644 --- a/Model/lib/jbrowse/treeQM6a/tracks.conf +++ b/Model/lib/jbrowse/treeQM6a/tracks.conf @@ -1,11 +1,8 @@ [tracks.treeQM6a_bld55Transcripts_transcript_sequences_RSRC] -query.feature=alignment:sequence -query.edName='treeQM6a_bld55Transcripts_transcript_sequences_RSRC' category=Gene Models key=Trichoderma reesei QM6a build 55 models -storeClass=JBrowse/Store/SeqFeature/REST -subParts=block -baseUrl=/a/service/jbrowse +storeClass=JBrowse/Store/SeqFeature/GFF3Tabix +urlTemplate=/a/service/jbrowse/store?data=TreeseiQM6a/alignedTranscripts/gff/treeQM6a_bld55Transcripts_transcript_sequences_RSRC/treeQM6a_bld55Transcripts_transcript_sequences_RSRC.gff.gz type=JBrowse/View/Track/CanvasFeatures glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript style.utrColor=grey diff --git a/Model/lib/jbrowse/tvagG3/tracks.conf b/Model/lib/jbrowse/tvagG3/tracks.conf deleted file mode 100644 index 0f04ad18b..000000000 --- a/Model/lib/jbrowse/tvagG3/tracks.conf +++ /dev/null @@ -1,14 +0,0 @@ -[tracks.TransposableElements] -query.feature=alignment:TransposableElements -category=Sequence Analysis -metadata.subcategory=Sequence sites, features and motifs -key=Transposable Elements -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/CanvasFeatures -glyph=JBrowse/View/FeatureGlyph/Box -metadata.trackType=Segments -displayMode=normal -style.color=black -# style.strandArrow=false -onClick.content={transposonFxn} diff --git a/Model/lib/jbrowse/tvagG32022/tracks.conf b/Model/lib/jbrowse/tvagG32022/tracks.conf deleted file mode 100644 index dbdc6beb3..000000000 --- a/Model/lib/jbrowse/tvagG32022/tracks.conf +++ /dev/null @@ -1,20 +0,0 @@ -[tracks.MobileElementFeatures] -query.feature=gff:basic -query.edName='tvagG32022_TE_GFF_RSRC' -category=Sequence Analysis -metadata.subcategory=Sequence sites, features and motifs -key=Transposable Elements -storeClass=JBrowse/Store/SeqFeature/REST -baseUrl=/a/service/jbrowse -type=JBrowse/View/Track/CanvasFeatures -glyph=JBrowse/View/FeatureGlyph/Box -metadata.trackType=Segments -displayMode=normal -style.color=black -style.strandArrow=false -#onClick.content={transposonFxn} -#metadata.dataset=Fitness during the T. gondii lytic cycle. (Genome-Wide CRISPR Screen) -#fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("tgonGT1_CrisprScreen_GFF_topLevel_RSRC", "Fitness during the T. gondii lytic cycle. (Genome-Wide CRISPR Screen)"); } - - - diff --git a/Model/lib/perl/JBrowseTrackConfig/CnvArrayTrackConfig.pm b/Model/lib/perl/JBrowseTrackConfig/CnvArrayTrackConfig.pm index 8f9e9db80..b0bb12dc1 100644 --- a/Model/lib/perl/JBrowseTrackConfig/CnvArrayTrackConfig.pm +++ b/Model/lib/perl/JBrowseTrackConfig/CnvArrayTrackConfig.pm @@ -3,8 +3,6 @@ use base qw(ApiCommonModel::Model::JBrowseTrackConfig::CoverageTrackConfig); use strict; use warnings; -use ApiCommonModel::Model::JBrowseTrackConfig::RestStore; - sub getName {$_[0]->{name}} sub setName {$_[0]->{name} = $_[1] } @@ -19,25 +17,9 @@ sub new { $datasetConfig->setCategory("Genetic Variation"); $datasetConfig->setSubcategory("CGH Array"); - $self->setId("SNPs by coding potential"); - $self->setLabel("SNPs by coding potential"); + $self->setId($args->{key}); + $self->setLabel($args->{label}); $self->setName($args->{name}); - #$self->setDisplayType("JBrowse/View/Track/Wiggle/XYPlot"); - - my $name = $self->getName(); - - my $store; - - if($self->getApplicationType() eq 'jbrowse' || $self->getApplicationType() eq 'apollo') { - $store = ApiCommonModel::Model::JBrowseTrackConfig::RestStore->new($args); - $store->setQuery("cnv:ArrayJBrowse"); - $store->setQueryParamsHash({sample => $name}); - } - else { - # TODO - } - - $self->setStore($store); $self->setTrackTypeDisplay("XYPlot"); diff --git a/Model/lib/perl/JBrowseTrackConfig/TransposableElements.pm b/Model/lib/perl/JBrowseTrackConfig/TransposableElements.pm new file mode 100644 index 000000000..42db295d5 --- /dev/null +++ b/Model/lib/perl/JBrowseTrackConfig/TransposableElements.pm @@ -0,0 +1,51 @@ +package ApiCommonModel::Model::JBrowseTrackConfig::TransposableElements; +use base qw(ApiCommonModel::Model::JBrowseTrackConfig::Segments); +use strict; +use warnings; + +use ApiCommonModel::Model::JBrowseTrackConfig::GFFStore; + +sub new { + my ($class, $args) = @_; + my $self = $class->SUPER::new($args); + + my $datasetConfig = $self->getDatasetConfigObj(); + $datasetConfig->setCategory("Sequence Analysis"); + $datasetConfig->setSubcategory("Sequence sites, features and motifs"); + + $self->setId("Transposable Elements"); + $self->setLabel("Transposable Elements"); + + my $store; + + if($self->getApplicationType() eq 'jbrowse' || $self->getApplicationType() eq 'apollo') { + $store = ApiCommonModel::Model::JBrowseTrackConfig::GFFStore->new($args); + } + else { + $store = ApiCommonModel::Model::JBrowseTrackConfig::GFFStore->new($args); + } + + $self->setStore($store); + + $self->setColor("goldenrod"); + + my $detailsFunction = "{transposableElementDetailsFxn}"; + $self->setOnClickContent($detailsFunction); + $self->setViewDetailsContent($detailsFunction); + + return $self; +} + + +# TODO: +sub getJBrowse2Object{ + my $self = shift; + + my $jbrowse2Object = $self->SUPER::getJBrowse2Object(); + + + return $jbrowse2Object; +} + + +1; diff --git a/Model/lib/perl/JbrowseOrgSpecificAaTracks.pm b/Model/lib/perl/JbrowseOrgSpecificAaTracks.pm index 832d1e039..678e50e14 100644 --- a/Model/lib/perl/JbrowseOrgSpecificAaTracks.pm +++ b/Model/lib/perl/JbrowseOrgSpecificAaTracks.pm @@ -37,7 +37,7 @@ sub processOrganism { &addSignalPeptide($result, $datasetProps, $webservicesDir, $nameForFileName, $projectName, $applicationType, $buildNumber); &addTmhmm($result, $datasetProps, $webservicesDir, $nameForFileName, $projectName, $applicationType, $buildNumber); &addLowComplexity($result, $datasetProps, $webservicesDir, $nameForFileName, $projectName, $applicationType, $buildNumber); - &addHydropathy($result, $datasetProps, $webservicesDir, $nameForFileName, $projectName, $applicationType, $buildNumber); + &addSecondaryStructureHelix($result, $datasetProps, $webservicesDir, $nameForFileName, $projectName, $applicationType, $buildNumber); &addSecondaryStructureCoil($result, $datasetProps, $webservicesDir, $nameForFileName, $projectName, $applicationType, $buildNumber); &addSecondaryStructureStrand($result, $datasetProps, $webservicesDir, $nameForFileName, $projectName, $applicationType, $buildNumber); @@ -46,7 +46,8 @@ sub processOrganism { } if ($isReference eq 'true' && $isHugeGenome eq 'false'){ - &addIedb($result, $datasetProps, $webservicesDir, $nameForFileName, $projectName, $applicationType, $buildNumber); + &addIedb($result, $datasetProps, $webservicesDir, $nameForFileName, $projectName, $applicationType, $buildNumber); + &addHydropathy($result, $datasetProps, $webservicesDir, $nameForFileName, $projectName, $applicationType, $buildNumber); } &addProteinExpressionMassSpec($result, $datasetProps, $webservicesDir, $nameForFileName, $projectName, $applicationType, $buildNumber); diff --git a/Model/lib/perl/JbrowseOrgSpecificNaTracks.pm b/Model/lib/perl/JbrowseOrgSpecificNaTracks.pm index 49e177d95..8dfdd59e0 100644 --- a/Model/lib/perl/JbrowseOrgSpecificNaTracks.pm +++ b/Model/lib/perl/JbrowseOrgSpecificNaTracks.pm @@ -24,6 +24,7 @@ use ApiCommonModel::Model::JBrowseTrackConfig::SyntenyTrackConfig; use ApiCommonModel::Model::JBrowseTrackConfig::LongReadRNASeqTrackConfig; use ApiCommonModel::Model::JBrowseTrackConfig::AntiSmashTrackConfig; use ApiCommonModel::Model::JBrowseTrackConfig::LowComplexityTrackConfig; +use ApiCommonModel::Model::JBrowseTrackConfig::TransposableElements; use ApiCommonModel::Model::JBrowseTrackConfig::TandemRepeatsTrackConfig; use ApiCommonModel::Model::JBrowseTrackConfig::EstTrackConfig; use ApiCommonModel::Model::JBrowseTrackConfig::OrfTrackConfig; @@ -56,6 +57,7 @@ sub processOrganism { &addReferenceSequence($applicationType, $result, $nameForFileNames, $projectName, $buildNumber); &addScaffolds($datasetProps, $applicationType, $result, $nameForFileNames, $projectName, $buildNumber); &addCentromere($datasetProps, $applicationType, $result, $nameForFileNames, $projectName, $buildNumber); + &addTransposableElements($datasetProps, $applicationType, $result, $nameForFileNames, $projectName, $buildNumber); &addUnifiedMassSpec($datasetProps, $applicationType, $result, $nameForFileNames, $projectName, $buildNumber); &addUnifiedSnp($datasetProps, $applicationType, $result); @@ -96,7 +98,7 @@ sub processOrganism { &addApolloGFF($dbh, $result, $organismAbbrev, $applicationType); } - &addMergedRnaSeq($dbh, $result, $datasetProperties, $projectName, $nameForFileNames, $organismAbbrev, $buildNumber); + &addMergedRnaSeq($result, $datasetProperties, $projectName, $nameForFileNames, $organismAbbrev, $buildNumber); &addLongReadRNASeq($result, $datasetProperties, $nameForFileNames, $webservicesDir, $projectName, $buildNumber, $applicationType); @@ -109,7 +111,7 @@ sub processOrganism { # other organism specific tracks if($organismAbbrev eq 'tcruCLBrenerEsmeraldo-like') { - &addCnvArray($dbh, $result, $projectName, $applicationType); + &addCnvArray($result, $projectName, $applicationType, $webservicesDir, $nameForFileNames, $buildNumber); } # TODO: Add back #if ($isAnnotated eq 'true'){ @@ -213,7 +215,7 @@ sub addApolloGFF { } sub addMergedRnaSeq { - my ($dbh, $result, $datasetProperties, $projectName, $nameForFileNames, $organismAbbrev, $buildNumber) = @_; + my ($result, $datasetProperties, $projectName, $nameForFileNames, $organismAbbrev, $buildNumber) = @_; my @urlArray; my $genomeName; @@ -236,7 +238,7 @@ sub addMergedRnaSeq { my $keyName = $bigwigFileName; $keyName =~ s/_/ /g; - my $bigWigRelativePath = "/var/www/Common/apiSiteFilesMirror/webServices/${projectName}/build-${buildNumber}/${nameForFileNames}/bigwig/${sampleName}/mergedBigwigs/*"; + my $bigWigRelativePath = "/var/www/Common/apiSiteFilesMirror/webServices/${projectName}/build-${buildNumber}/${nameForFileNames}/bulkrnaseq/bigwig/${sampleName}/mergedBigwigs/*"; my @bigwigFiles = glob($bigWigRelativePath); my $shortAttribution = $rnaSeqDatasets->{$dataset}->{shortAttribution}; foreach(@bigwigFiles){ @@ -244,12 +246,12 @@ sub addMergedRnaSeq { my $bigwigName = (split '/', $bigwigPath)[-1]; my $shortBigwigName = $bigwigName; my $shortBigwigName = substr($shortBigwigName,0, -3); - my $bigwigUrl = "/a/service/jbrowse/store?data=" . uri_escape_utf8("${nameForFileNames}/bigwig/${sampleName}/mergedBigwigs/${bigwigName}"); + my $bigwigUrl = "/a/service/jbrowse/store?data=" . uri_escape_utf8("${nameForFileNames}/bulkrnaseq/bigwig/${sampleName}/mergedBigwigs/${bigwigName}"); my $template = { url=>${bigwigUrl}, name=> ${shortBigwigName}, color=> 'black' }; push (@urlArray, $template); push (@urlArrayProject, $template); } - } + } ### Print out combinedRNAseq track for organism my $arrayLength = @urlArray; @@ -498,11 +500,27 @@ sub addCentromere { } +sub addTransposableElements { + my ($datasetProps, $applicationType, $result, $nameForFileNames, $projectName, $buildNumber) = @_; + my $hasTransposableElements = $datasetProps->{hasTransposableElements} ? $datasetProps->{hasTransposableElements} : 0; + if($hasTransposableElements == 1) { + my $relativePathToGffFile = "${nameForFileNames}/genomeBrowser/gff/transposableElements.gff.gz"; + my $track = ApiCommonModel::Model::JBrowseTrackConfig::TransposableElements->new({ + project_name => $projectName, + build_number => $buildNumber, + relative_path_to_file => $relativePathToGffFile, + application_type => $applicationType, + })->getConfigurationObject(); + push @{$result->{tracks}}, $track; + } +} + + sub addScaffolds { my ($datasetProps, $applicationType, $result, $nameForFileNames, $projectName, $buildNumber) = @_; my $hasScaffold = $datasetProps->{hasScaffoldGenome} ? $datasetProps->{hasScaffoldGenome} : 0; if($hasScaffold == 1) { - my $relativePathToGffFile = "${nameForFileNames}/genomeBrowser/gff/scaffolds.gff.gz"; + my $relativePathToGffFile = "${nameForFileNames}/genomeBrowser/gff/scaffoldGenome.gff.gz"; my $track = ApiCommonModel::Model::JBrowseTrackConfig::ScaffoldsTrackConfig->new({ application_type => $applicationType, project_name => $projectName, @@ -903,34 +921,34 @@ sub makeChipChipSmoothed { sub addCnvArray { - my ($dbh, $result, $projectName, $applicationType) = @_; - - my $sql = "select distinct pan.name -from study.protocolappnode pan - , study.study s - , study.studylink sl -where pan.PROTOCOL_APP_NODE_ID = sl.PROTOCOL_APP_NODE_ID -and sl.study_id = s.study_id -and s.name like 'tcruCLBrenerEsmeraldo-like_cghArrayExper_Tarelton_GSE23576_CNV_RSRC%' -order by pan.name"; - my $sh = $dbh->prepare($sql); - $sh->execute(); + my ($result, $projectName, $applicationType, $webservicesDir, $nameForFileNames, $buildNumber) = @_; + + my $datasetName = 'tcruCLBrenerEsmeraldo-like_cghArrayExper_Tarelton_GSE23576_CNV_RSRC'; + my $bigwigDir = "${webservicesDir}/${projectName}/build-${buildNumber}/${nameForFileNames}/cghArray/bigwig/${datasetName}"; my $summary = "Comparative Genomic Hybridization to determine regions of significant Copy Number Variation in T. cruzi strains with strain CL Brener as reference. Type I strains used include: Brazil, Chinata, Colombiana, M78, Montalvania, PalDa1 (clone 9), SylvioX10/4, TCC, TEDa2 (clone 4), TEP6 (clone 5). Type II-VI strains used include: Esmeraldo, M5631, Tu18 (clone 1), Tulahuen, wtCL, Y. Scores from Type I strain is shown in Green and from Type II-VI are show in Brown. Score value represents the number of strains showing CNV , with a postive score implying amplification and a negative score implying deletion with respect to CL Brener. CNV criteria: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5. For more details refer the following manuscript: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization "; - while(my ($dataset) = $sh->fetchrow_array()) { + foreach my $bwFile (glob("${bigwigDir}/*.bw")) { + my $sample = $bwFile; + $sample =~ s{.*/}{}; + $sample =~ s/\.bw$//; + + my $relativePath = "${nameForFileNames}/cghArray/bigwig/${datasetName}/${sample}.bw"; my $cnv = ApiCommonModel::Model::JBrowseTrackConfig::CnvArrayTrackConfig->new({ - dataset_name => $dataset, - study_display_name => "Comparative Genomic Hybridizations of 33 strains", - description => $summary, - application_type => $applicationType, - name => $dataset, - })->getConfigurationObject(); + dataset_name => $datasetName, + study_display_name => "Comparative Genomic Hybridizations of 33 strains", + description => $summary, + application_type => $applicationType, + name => $sample, + label => $sample, + key => $sample, + relative_path_to_file => $relativePath, + project_name => $projectName, + build_number => $buildNumber, + })->getConfigurationObject(); push @{$result->{tracks}}, $cnv; - } - $sh->finish(); } diff --git a/Model/lib/psql/webready/comparative/ProteinSequenceGroup.psql b/Model/lib/psql/webready/comparative/ProteinSequenceGroup.psql index de2df5a82..6288c1b92 100644 --- a/Model/lib/psql/webready/comparative/ProteinSequenceGroup.psql +++ b/Model/lib/psql/webready/comparative/ProteinSequenceGroup.psql @@ -1,6 +1,6 @@ create table :SCHEMA.ProteinSequenceGroup as SELECT - distinct(aas.source_id) AS full_id, + aas.source_id AS full_id, aas.source_id, aas.aa_sequence_id, length(aas.sequence) as length, @@ -63,7 +63,7 @@ ) taxon, ( - SELECT aas.aa_sequence_id, + SELECT DISTINCT ON (aas.aa_sequence_id) aas.aa_sequence_id, CASE WHEN ores.resource_name IN ('AmoebaDB','CryptoDB','FungiDB','GiardiaDB','HostDB','MicrosporidiaDB', 'PlasmoDB','PiroplasmaDB','ToxoDB','TrichDB','TriTrypDB','VectorBase') @@ -84,7 +84,6 @@ AND ogseq.group_id = o.group_id AND aas.aa_sequence_id = urls.aa_sequence_id AND taxon.orthomcl_taxon_id = aas.taxon_id - AND aas.taxon_id in (select distinct(eas.taxon_id) from apidb.organism og, dots.aasequence eas where eas.taxon_id = og.taxon_id) ; alter table :SCHEMA.ProteinSequenceGroup diff --git a/Model/lib/psql/webready/orgSpecific/GeneProduct_p.psql b/Model/lib/psql/webready/orgSpecific/GeneProduct_p.psql index 21f94fba3..18a2a1c39 100644 --- a/Model/lib/psql/webready/orgSpecific/GeneProduct_p.psql +++ b/Model/lib/psql/webready/orgSpecific/GeneProduct_p.psql @@ -97,12 +97,43 @@ create unlogged table :SCHEMA.:CLEAN_ORG_ABBREVGeneFeatureProductTmp as GROUP BY gf.source_id ), - -- Priority 6: All gene products (concatenated) - gene_all AS ( + -- Priority 6: Preferred gene products (is_preferred=1, concatenated) + gene_preferred_all AS ( SELECT gf.source_id, SUBSTR(STRING_AGG(DISTINCT gfp.product, ', ' ORDER BY gfp.product), 1, 4000) as product, 6 as source_rule, COUNT(DISTINCT gfp.product) as value_count, + 'preferred_gene' as rule_description + FROM :SCHEMA.:CLEAN_ORG_ABBREVGeneFeatureProductTmp gf + INNER JOIN apidb.GeneFeatureProduct gfp ON gfp.na_feature_id = gf.na_feature_id + WHERE gfp.is_preferred = 1 + AND gfp.product IS NOT NULL + AND gfp.product != 'hypothetical protein' + GROUP BY gf.source_id + ), + + -- Priority 7: Preferred transcript products (is_preferred=1, concatenated) + transcript_preferred_all AS ( + SELECT gf.source_id, + SUBSTR(STRING_AGG(DISTINCT tp.product, ', ' ORDER BY tp.product), 1, 4000) as product, + 7 as source_rule, + COUNT(DISTINCT tp.product) as value_count, + 'preferred_transcript' as rule_description + FROM :SCHEMA.:CLEAN_ORG_ABBREVGeneFeatureProductTmp gf + INNER JOIN dots.Transcript t ON t.parent_id = gf.na_feature_id + INNER JOIN apidb.TranscriptProduct tp ON tp.na_feature_id = t.na_feature_id + WHERE tp.is_preferred = 1 + AND tp.product IS NOT NULL + AND tp.product != 'hypothetical protein' + GROUP BY gf.source_id + ), + + -- Priority 8: All gene products (concatenated) + gene_all AS ( + SELECT gf.source_id, + SUBSTR(STRING_AGG(DISTINCT gfp.product, ', ' ORDER BY gfp.product), 1, 4000) as product, + 8 as source_rule, + COUNT(DISTINCT gfp.product) as value_count, 'all_gene' as rule_description FROM :SCHEMA.:CLEAN_ORG_ABBREVGeneFeatureProductTmp gf INNER JOIN apidb.GeneFeatureProduct gfp ON gfp.na_feature_id = gf.na_feature_id @@ -111,11 +142,11 @@ create unlogged table :SCHEMA.:CLEAN_ORG_ABBREVGeneFeatureProductTmp as GROUP BY gf.source_id ), - -- Priority 7: All transcript products (concatenated) + -- Priority 9: All transcript products (concatenated) transcript_all AS ( SELECT gf.source_id, SUBSTR(STRING_AGG(DISTINCT tp.product, ', ' ORDER BY tp.product), 1, 4000) as product, - 7 as source_rule, + 9 as source_rule, COUNT(DISTINCT tp.product) as value_count, 'all_transcript' as rule_description FROM :SCHEMA.:CLEAN_ORG_ABBREVGeneFeatureProductTmp gf @@ -126,31 +157,17 @@ create unlogged table :SCHEMA.:CLEAN_ORG_ABBREVGeneFeatureProductTmp as GROUP BY gf.source_id ), - -- Priority 8: Base gene product field + -- Priority 10: Base gene product field gene_base AS ( SELECT gf.source_id, gf.product, - 8 as source_rule, + 10 as source_rule, 1 as value_count, 'base_gene' as rule_description FROM :SCHEMA.:CLEAN_ORG_ABBREVGeneFeatureProductTmp gf WHERE gf.product IS NOT NULL ), - -- Priority 9: Base transcript product field (concatenated) - transcript_base AS ( - SELECT gf.source_id, - SUBSTR(STRING_AGG(DISTINCT t.product, ', ' ORDER BY t.product), 1, 4000) as product, - 9 as source_rule, - COUNT(DISTINCT t.product) as value_count, - 'base_transcript' as rule_description - FROM :SCHEMA.:CLEAN_ORG_ABBREVGeneFeatureProductTmp gf - INNER JOIN dots.Transcript t ON t.parent_id = gf.na_feature_id - WHERE t.product IS NOT NULL - AND t.product != 'hypothetical protein' - GROUP BY gf.source_id - ), - -- Combine all priorities all_products AS ( SELECT * FROM gene_curated_preferred @@ -158,10 +175,11 @@ create unlogged table :SCHEMA.:CLEAN_ORG_ABBREVGeneFeatureProductTmp as UNION ALL SELECT * FROM transcript_curated_preferred_one_to_one UNION ALL SELECT * FROM transcript_curated_any_one_to_one UNION ALL SELECT * FROM gene_arba + UNION ALL SELECT * FROM gene_preferred_all + UNION ALL SELECT * FROM transcript_preferred_all UNION ALL SELECT * FROM gene_all UNION ALL SELECT * FROM transcript_all UNION ALL SELECT * FROM gene_base - UNION ALL SELECT * FROM transcript_base ), -- Select highest priority product per gene @@ -173,7 +191,7 @@ create unlogged table :SCHEMA.:CLEAN_ORG_ABBREVGeneFeatureProductTmp as SELECT gf.source_id, COALESCE(rp.product, 'unspecified product') as product, COALESCE(rp.value_count, 0) as value_count, - COALESCE(rp.source_rule, 10) as source_rule, + COALESCE(rp.source_rule, 11) as source_rule, COALESCE(rp.rule_description, 'unspecified') as source_rule_description, ':PROJECT_ID' as project_id, ':ORG_ABBREV' as org_abbrev, diff --git a/Model/lib/psql/webready/orgSpecific/TranscriptProduct_p.psql b/Model/lib/psql/webready/orgSpecific/TranscriptProduct_p.psql index 1100910fc..63ccffe72 100644 --- a/Model/lib/psql/webready/orgSpecific/TranscriptProduct_p.psql +++ b/Model/lib/psql/webready/orgSpecific/TranscriptProduct_p.psql @@ -92,12 +92,42 @@ create unlogged table :SCHEMA.:CLEAN_ORG_ABBREVTranscriptProductTmp as GROUP BY t.source_id ), - -- Priority 5: 1:1 + All gene products (concatenated) - gene_all_one_to_one AS ( + -- Priority 5: 1:1 + Preferred gene products (is_preferred=1, concatenated) + gene_preferred_one_to_one AS ( SELECT oto.transcript_source_id as source_id, SUBSTR(STRING_AGG(DISTINCT gfp.product, ', ' ORDER BY gfp.product), 1, 4000) as product, 5 as source_rule, COUNT(DISTINCT gfp.product) as value_count, + 'preferred_gene_1to1' as rule_description + FROM one_to_one_transcripts oto + INNER JOIN apidb.GeneFeatureProduct gfp ON gfp.na_feature_id = oto.gene_na_feature_id + WHERE gfp.is_preferred = 1 + AND gfp.product IS NOT NULL + AND gfp.product != 'hypothetical protein' + GROUP BY oto.transcript_source_id + ), + + -- Priority 6: Preferred transcript products (is_preferred=1, concatenated) + transcript_preferred_all AS ( + SELECT t.source_id, + SUBSTR(STRING_AGG(DISTINCT tp.product, ', ' ORDER BY tp.product), 1, 4000) as product, + 6 as source_rule, + COUNT(DISTINCT tp.product) as value_count, + 'preferred_transcript' as rule_description + FROM :SCHEMA.:CLEAN_ORG_ABBREVTranscriptProductTmp t + INNER JOIN apidb.TranscriptProduct tp ON tp.na_feature_id = t.na_feature_id + WHERE tp.is_preferred = 1 + AND tp.product IS NOT NULL + AND tp.product != 'hypothetical protein' + GROUP BY t.source_id + ), + + -- Priority 7: 1:1 + All gene products (concatenated) + gene_all_one_to_one AS ( + SELECT oto.transcript_source_id as source_id, + SUBSTR(STRING_AGG(DISTINCT gfp.product, ', ' ORDER BY gfp.product), 1, 4000) as product, + 7 as source_rule, + COUNT(DISTINCT gfp.product) as value_count, 'all_gene_1to1' as rule_description FROM one_to_one_transcripts oto INNER JOIN apidb.GeneFeatureProduct gfp ON gfp.na_feature_id = oto.gene_na_feature_id @@ -106,11 +136,11 @@ create unlogged table :SCHEMA.:CLEAN_ORG_ABBREVTranscriptProductTmp as GROUP BY oto.transcript_source_id ), - -- Priority 6: All transcript products (concatenated) + -- Priority 8: All transcript products (concatenated) transcript_all AS ( SELECT t.source_id, SUBSTR(STRING_AGG(DISTINCT tp.product, ', ' ORDER BY tp.product), 1, 4000) as product, - 6 as source_rule, + 8 as source_rule, COUNT(DISTINCT tp.product) as value_count, 'all_transcript' as rule_description FROM :SCHEMA.:CLEAN_ORG_ABBREVTranscriptProductTmp t @@ -120,11 +150,11 @@ create unlogged table :SCHEMA.:CLEAN_ORG_ABBREVTranscriptProductTmp as GROUP BY t.source_id ), - -- Priority 7: 1:1 + Base gene product field + -- Priority 9: 1:1 + Base gene product field gene_base_one_to_one AS ( SELECT oto.transcript_source_id as source_id, gf.product, - 7 as source_rule, + 9 as source_rule, 1 as value_count, 'base_gene_1to1' as rule_description FROM one_to_one_transcripts oto @@ -132,11 +162,11 @@ create unlogged table :SCHEMA.:CLEAN_ORG_ABBREVTranscriptProductTmp as WHERE gf.product IS NOT NULL ), - -- Priority 8: Base transcript product field + -- Priority 10: Base transcript product field transcript_base AS ( SELECT t.source_id, t.product, - 8 as source_rule, + 10 as source_rule, 1 as value_count, 'base_transcript' as rule_description FROM :SCHEMA.:CLEAN_ORG_ABBREVTranscriptProductTmp t @@ -149,6 +179,8 @@ create unlogged table :SCHEMA.:CLEAN_ORG_ABBREVTranscriptProductTmp as UNION ALL SELECT * FROM gene_curated_any_one_to_one UNION ALL SELECT * FROM transcript_curated_preferred UNION ALL SELECT * FROM transcript_curated_any + UNION ALL SELECT * FROM gene_preferred_one_to_one + UNION ALL SELECT * FROM transcript_preferred_all UNION ALL SELECT * FROM gene_all_one_to_one UNION ALL SELECT * FROM transcript_all UNION ALL SELECT * FROM gene_base_one_to_one @@ -164,7 +196,7 @@ create unlogged table :SCHEMA.:CLEAN_ORG_ABBREVTranscriptProductTmp as SELECT t.source_id, COALESCE(rp.product, 'unspecified product') as product, COALESCE(rp.value_count, 0) as value_count, - COALESCE(rp.source_rule, 9) as source_rule, + COALESCE(rp.source_rule, 11) as source_rule, COALESCE(rp.rule_description, 'unspecified') as source_rule_description, ':PROJECT_ID' as project_id, ':ORG_ABBREV' as org_abbrev, diff --git a/Model/lib/wdk/model/questions/geneQuestions.xml b/Model/lib/wdk/model/questions/geneQuestions.xml index 7690d0569..45f3f73e2 100644 --- a/Model/lib/wdk/model/questions/geneQuestions.xml +++ b/Model/lib/wdk/model/questions/geneQuestions.xml @@ -931,6 +931,84 @@ In the analysis carried out by Alsford et al., pseudogenes, genes annotated as " + + + + + + + + + + + + + + + + + + + + + + + + $$sequence_id$$:$$cluster_start$$-$$cluster_end$$ + ]]> + + + + + + +
+ + In addition to primary metabolites essential for growth and survival, fungi and some other microorganisms produce secondary metabolites. These often provide competitive advantages for the microorganism in its environment. They are also of interest as an important source of natural products. These compounds are typically encoded by co-located and co-expressed groups of genes that function together to build, modify, and export the final molecule. This co-located group is called a biosynthetic gene cluster (BGC). Well-known examples of secondary metabolites include antibiotics like penicillin and erythromycin, antifungals, and immunosuppressants like rapamycin.

+ + antiSMASH is a bioinformatics tool to identify and annotate biosynthetic gene clusters. It works by searching for signature biosynthetic genes whose sequences are well conserved across known clusters. When it detects one of these signature genes, it defines a genomic region around it, predicts the cluster boundaries, and annotates every gene within that region with a predicted function. It then compares the identified cluster against a database of known BGCs to predict what compound the cluster might produce.

+ + Cluster Category
+ The cluster category groups biosynthetic gene clusters (BGCs) into broad classes based on the type of natural product they produce. This is predicted based on the biochemical machinery represented in the cluster.

+ + Common categories you are likely to see include:
+
    +
  • PKS (Polyketide synthases): Clusters that synthesize secondary metabolites comprising complex chains of alternating ketone and methylene groups. These molecules often function as antibiotics, antifungals, or anticancer compounds. Examples include erythromycin and rapamycin.
    • +
  • NRPS (Nonribosomal peptide synthases): Clusters that synthesize secondary metabolites comprising amino acids, including non-proteinogenic amino acids, polymerized without using ribosomes. These molecules often function as antibiotics or siderophores. Examples include penicillin and vancomycin.
    • +
  • Terpenes: Clusters that make terpenoids, a huge and diverse class of compounds derived from isoprene units, including sterols, pigments, and volatile compounds.
    • +
  • RiPP (Ribosomally synthesised and post-translationally modified peptides): These clusters create compounds from small peptides that are initially made by the ribosome and then heavily modified. Examples include lanthipeptides and bacteriocins.
    • +
  • Other: Clusters whose products cannot be categorized or that use a combination of structures from multiple categories.
    • +


+ + Annotation
+ The annotation describes what a specific gene or protein within the cluster is predicted to do based on sequence similarity to known proteins.

+ + Common annotations you are likely to see include:
+
    +
  • Biosynthetic: These are the signature biosynthetic genes that define a cluster and predict its function. These may be referred to as core or backbone genes.
    • +
  • Biosynthetic additional: These are additional biosynthetic genes that further modify the primary product of a cluster (tailoring or decorating enzymes), or aid production of the product by supplying cofactors or substrates.
    • +
  • Regulatory: These are transcription factors or other regulatory elements that control expression of this cluster.
    • +
  • Resistance: These genes protect the organism from its own toxic products. Examples include efflux pumps or enzymes that modify the product futher to protect the host.
    • +
  • Transport: These genes transport the product to its final location.
    • +
  • Other: This label is applied by antiSMASH when a gene has similarity to genes that appear in other BCGs but where the role of the gene within the BCG is not understood.
    • +
  • Unknown: This category is used for genes with no detectable similarity to antiSMASH models, and which have therefore not been annotated by antiSMASH.
    • +


+ +Read more about antismash here

+ ]]> + + + diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index fa686ea6a..c59f94e3e 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -5104,6 +5104,29 @@ products of your selected type (or types).

+ + + The cluster category describes what kind of molecule the cluster is likely to make based on the biochemical machinery represnted in the cluster. Select one or more secondary metabolite cluster categories to explore. + + + + + The annotation describes the function of a specific gene within a biosynthetic cluster. Select one or more annotations to explore. + + + @@ -8363,7 +8386,9 @@ products of your selected type (or types).

WHEN 'Hagai' THEN 'MPMP' ELSE evidence_code END as term - FROM dots.aaSequenceEnzymeClass + FROM dots.aaSequenceEnzymeClass asec, webready.TranscriptAttributes_p ta + WHERE ta.aa_sequence_id = asec.aa_sequence_id + AND (ta.project_id = '@PROJECT_ID@' or 'UniDB' = '@PROJECT_ID@') @@ -9711,6 +9736,62 @@ end as term + + + + + + + + + + + + + + + + + + + + + diff --git a/Model/lib/wdk/model/questions/params/organismParams.xml b/Model/lib/wdk/model/questions/params/organismParams.xml index 5fb56512b..d3dae0663 100644 --- a/Model/lib/wdk/model/questions/params/organismParams.xml +++ b/Model/lib/wdk/model/questions/params/organismParams.xml @@ -438,6 +438,21 @@ + + Select the organism(s) to search. + + pruneNodesWithSingleExtendingChild + showOnlyPreferredOrganisms + + + @@ -1170,6 +1185,31 @@ + + + + + + + + + diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index c0163792a..a11b3f463 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -715,7 +715,7 @@ - + @@ -743,6 +743,7 @@ WHERE LOWER(gi.id) = LOWER(ds.gene_source_id) ) t WHERE t.gene = ta.gene_source_id + and (ta.project_id = '@PROJECT_ID@' or 'UniDB' = '@PROJECT_ID@') GROUP BY ta.gene_source_id, ta.source_id, ta.project_id UNION SELECT @@ -753,6 +754,7 @@ MIN(ds.dataset_value_order) as dataset_order FROM apidbtuning.TranscriptAttributes ta, ( $$ds_gene_ids$$ ) ds WHERE lower(ta.source_id) = LOWER(ds.gene_source_id ) + and (ta.project_id = '@PROJECT_ID@' or 'UniDB' = '@PROJECT_ID@') GROUP BY ta.gene_source_id, ta.source_id, ta.project_id ) t GROUP BY source_id, gene_source_id, project_id @@ -3490,6 +3492,8 @@ $$regulated_dir$$ (greatest($$hard_floor$$,one.chosen) / greatest($$hard_floor$$,two.chosen)) >= $$fold_change$$ OR $$regulated_dir$$ (-(greatest($$hard_floor$$,two.chosen) / greatest($$hard_floor$$,one.chosen))) >= $$fold_change$$ ) + AND one.average + one.chosen + $$hard_floor$$ > 0 + AND two.average + two.chosen + $$hard_floor$$ > 0 ]]> @@ -5769,6 +5773,85 @@ select distinct ta.gene_source_id + + + + + + + + + + + + + + + + + + + + ', + gc2.sequence_id, ':', gc2.cluster_start, '-', gc2.cluster_end, '' + ), + ', ' ORDER BY gc2.cluster_start + ) AS overlapping_clusters + FROM ranked r + JOIN gene_clusters gc2 + ON gc2.source_id = r.source_id + AND gc2.antismash_cluster_id != r.antismash_cluster_id + WHERE r.rn = 1 + GROUP BY r.source_id + ) + SELECT r.source_id, r.gene_source_id, r.project_id, + 10 AS wdk_weight, 'Y' AS matched_result, + r.category, r.antismash_annotation, r.cluster_start, r.cluster_end, r.sequence_id, + r.org_abbrev, + GREATEST(r.cluster_start - 1000, 1) AS cluster_context_start, + r.cluster_end + 1000 AS cluster_context_end, + COALESCE(go.overlapping_clusters, 'No') AS overlapping_clusters + FROM ranked r + LEFT JOIN gene_overlaps go ON go.source_id = r.source_id + WHERE r.rn = 1 + ]]> + + + diff --git a/Model/lib/wdk/model/records/commentTableQueries.xml b/Model/lib/wdk/model/records/commentTableQueries.xml index 28f63e8c4..2c578927d 100644 --- a/Model/lib/wdk/model/records/commentTableQueries.xml +++ b/Model/lib/wdk/model/records/commentTableQueries.xml @@ -66,6 +66,7 @@ + diff --git a/Model/lib/wdk/model/records/geneAttributeQueries.xml b/Model/lib/wdk/model/records/geneAttributeQueries.xml index b02229dcc..8e1e2dbb0 100644 --- a/Model/lib/wdk/model/records/geneAttributeQueries.xml +++ b/Model/lib/wdk/model/records/geneAttributeQueries.xml @@ -163,7 +163,8 @@ WHERE ga.org_abbrev IN (%%PARTITION_KEYS%%) FROM apidbtuning.GeneId a, apidbtuning.GeneAttributes ga WHERE a.unique_mapping = 1 AND a.gene = ga.source_id - ]]> + AND (ga.project_id = '@PROJECT_ID@' or 'UniDB' = '@PROJECT_ID@') + ]]> diff --git a/Model/lib/wdk/model/records/geneRecord.xml b/Model/lib/wdk/model/records/geneRecord.xml index af8f7b216..00d5e450e 100644 --- a/Model/lib/wdk/model/records/geneRecord.xml +++ b/Model/lib/wdk/model/records/geneRecord.xml @@ -3174,6 +3174,18 @@ name" internal="true"/> + + + + + + +
+ diff --git a/Model/lib/wdk/model/records/geneTableQueries.xml b/Model/lib/wdk/model/records/geneTableQueries.xml index f70483a85..8f8ac9d61 100644 --- a/Model/lib/wdk/model/records/geneTableQueries.xml +++ b/Model/lib/wdk/model/records/geneTableQueries.xml @@ -647,6 +647,7 @@ + @@ -780,6 +781,7 @@ + @@ -833,7 +835,7 @@ FROM webready.GeneAttributes_p ga , @VDI_CONTROL_SCHEMA@.AvailableUserDatasets da - , @VDI_DATASETS_SCHEMA@.UD_NAFEATUREEXPRESSION naf + , @VDI_DATASETS_SCHEMA@.UD_NAFEATUREEXPRESSION naf , @VDI_DATASETS_SCHEMA@.UD_PROTOCOLAPPNODE pan , @VDI_DATASETS_SCHEMA@.UD_PROFILESET ps , ( @@ -961,13 +963,14 @@ + - - + + @@ -976,7 +979,7 @@ - + - - + + @@ -1139,6 +1143,7 @@ from ( + @@ -2534,7 +2539,7 @@ from ( JOIN apidbtuning.TranscriptAttributes ota ON tog.source_id = ota.source_id JOIN apidb.Organism o ON ota.taxon_id = o.taxon_id WHERE gog.org_abbrev IN (%%PARTITION_KEYS%%) - AND (ota.project_id = '@PROJECT_ID@' or 'UniDB' = '@PROJECT_ID@') + AND ota.project_id = gog.project_id --only include orthologs within project ), OrthologousTranscripts as ( SELECT distinct all_pairs.* , COALESCE(syn_pairs.is_syntenic, 0) AS is_syntenic @@ -4844,5 +4849,37 @@ FROM webready.GeneAttributes_p ga, ( + + + + + + + + + + + + + diff --git a/Model/lib/wdk/model/records/pathwayTableQueries.xml b/Model/lib/wdk/model/records/pathwayTableQueries.xml index f076d094f..e220efdfa 100644 --- a/Model/lib/wdk/model/records/pathwayTableQueries.xml +++ b/Model/lib/wdk/model/records/pathwayTableQueries.xml @@ -169,7 +169,7 @@ @@ -198,9 +198,17 @@ diff --git a/Model/lib/wdk/ontology/individuals.txt b/Model/lib/wdk/ontology/individuals.txt index a3136ed84..a0f9e4ec1 100644 --- a/Model/lib/wdk/ontology/individuals.txt +++ b/Model/lib/wdk/ontology/individuals.txt @@ -75,6 +75,7 @@ TranscriptRecordClasses.TranscriptRecordClass.GeneQuestions.GenesByGeneType http TranscriptRecordClasses.TranscriptRecordClass.GeneQuestions.GenesByIntronJunctions http://edamontology.org/topic_0114 Gene Structure TranscriptRecordClasses.TranscriptRecordClass search GeneQuestions.GenesByIntronJunctions menu webservice TranscriptRecordClasses.TranscriptRecordClass.GeneQuestions.GenesByGeneModelChars http://edamontology.org/topic_0114 Gene Structure TranscriptRecordClasses.TranscriptRecordClass search GeneQuestions.GenesByGeneModelChars menu webservice TranscriptRecordClasses.TranscriptRecordClass.GeneQuestions.GenesByGoTerm http://edamontology.org/topic_1775 Function analysis TranscriptRecordClasses.TranscriptRecordClass search GeneQuestions.GenesByGoTerm menu webservice +TranscriptRecordClasses.TranscriptRecordClass.GeneQuestions.GenesBySecondaryMetabolites http://edamontology.org/topic_1775 Function analysis TranscriptRecordClasses.TranscriptRecordClass search GeneQuestions.GenesBySecondaryMetabolites menu webservice ## TEMPLATE_ANCHOR geneImageGoTermOntology TranscriptRecordClasses.TranscriptRecordClass.GeneQuestions.GenesByPhenotype_phenotype_QIAGEN_RSRC searchCategory-phenotype-curated phenotype TranscriptRecordClasses.TranscriptRecordClass search GeneQuestions.GenesByPhenotype_phenotype_QIAGEN_RSRC webservice TranscriptRecordClasses.TranscriptRecordClass.GeneQuestions.GenesByPhenotype_phenotype_DATA_RSRC searchCategory-phenotype-curated phenotype TranscriptRecordClasses.TranscriptRecordClass search GeneQuestions.GenesByPhenotype_phenotype_DATA_RSRC webservice @@ -235,7 +236,8 @@ GeneRecordClasses.GeneRecordClass.specialJbrowseUrl http://edamontology.org/topi GeneRecordClasses.GeneRecordClass.ExpressionGraphsDataTable http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table ExpressionGraphsDataTable gene record-internal GeneRecordClasses.GeneRecordClass.UserDatasetsTranscriptomicsGraphsDataTable http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table UserDatasetsTranscriptomicsGraphsDataTable gene record-internal GeneRecordClasses.GeneRecordClass.FacetMetadata http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table FacetMetadata gene record-internal -GeneRecordClasses.GeneRecordClass.FungiVBOrgLinkoutsTable http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table FungiVBOrgLinkoutsTable gene record-internal +GeneRecordClasses.GeneRecordClass.FungiVBOrgLinkoutsTable http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table FungiVBOrgLinkoutsTable gene record-internal +GeneRecordClasses.GeneRecordClass.SecondaryMetaboliteClusters http://edamontology.org/topic_1775 Function analysis GeneRecordClasses.GeneRecordClass table SecondaryMetaboliteClusters gene record download GeneRecordClasses.GeneRecordClass.ContXAxisMetadata http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table ContXAxisMetadata gene record-internal GeneRecordClasses.GeneRecordClass.ai_expression http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass attribute ai_expression gene 2 record @@ -296,7 +298,7 @@ GeneRecordClasses.GeneRecordClass.GOSlim http://edamontology.org/topic_1775 Func GeneRecordClasses.GeneRecordClass.GOTerms http://edamontology.org/topic_1775 Function analysis GeneRecordClasses.GeneRecordClass table GOTerms transcript record download GeneRecordClasses.GeneRecordClass.Y2hInteractions http://edamontology.org/topic_0128 Protein Interactions GeneRecordClasses.GeneRecordClass table Y2hInteractions gene record download GeneRecordClasses.GeneRecordClass.Orthologs http://edamontology.org/topic_3299 Evolutionary Biology GeneRecordClasses.GeneRecordClass table Orthologs gene record -GeneRecordClasses.GeneRecordClass.OrthologsLite http://edamontology.org/topic_3299 Evolutionary Biology GeneRecordClasses.GeneRecordClass table OrthologsLite gene download +GeneRecordClasses.GeneRecordClass.OrthologsLite http://edamontology.org/topic_3299 Evolutionary Biology GeneRecordClasses.GeneRecordClass table OrthologsLite gene GeneRecordClasses.GeneRecordClass.MetabolicPathwaysMPMP http://edamontology.org/topic_0753 Metabolic Pathways GeneRecordClasses.GeneRecordClass table MetabolicPathwaysMPMP transcript 1 record download GeneRecordClasses.GeneRecordClass.MetabolicPathways http://edamontology.org/topic_0753 Metabolic Pathways GeneRecordClasses.GeneRecordClass table MetabolicPathways transcript 2 record download GeneRecordClasses.GeneRecordClass.Alias http://edamontology.org/topic_0219 Curation and Annotation GeneRecordClasses.GeneRecordClass table Alias transcript record download diff --git a/Model/lib/xml/dataPlotter/queries.xml b/Model/lib/xml/dataPlotter/queries.xml index bfd7b77da..960232815 100644 --- a/Model/lib/xml/dataPlotter/queries.xml +++ b/Model/lib/xml/dataPlotter/queries.xml @@ -28,6 +28,7 @@ and pan.name like '%secondstrand%') or pan.name like '%unstranded%') and p.profile_set_name not like '%nonunique%' + and ps.node_type not like '%nonunique%' and p.profile_set_name = ps.study_name and ps.protocol_app_node_id = pan.protocol_app_node_id and p.dataset_name = dd.name @@ -89,11 +90,11 @@ diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index 59a14d1b2..7bcc493af 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -6,7 +6,7 @@ - + @@ -46,8 +46,8 @@ - - + + @@ -275,359 +275,6 @@ - - - - Provides correct gene products using priority-based cascading logic: - Priority 1: Preferred Curated GeneFeatureProduct (is_preferred=1, Sanger|VEuPathDB|Apollo) - Priority 2: Any Curated GeneFeatureProduct (Sanger|VEuPathDB|Apollo) - Priority 3: 1:1 Gene:Transcript + Preferred Curated TranscriptProduct (is_preferred=1, Sanger|VEuPathDB|Apollo) - Priority 4: 1:1 Gene:Transcript + Any Curated TranscriptProduct (Sanger|VEuPathDB|Apollo) - Priority 5: ARBA GeneFeatureProduct - Priority 6: All GeneFeatureProduct (concatenated) - Priority 7: All TranscriptProduct (concatenated) - Priority 8: GeneFeature.product (base field) - This is a global table (all organisms) - source_id is globally unique. - - - - - - - - - - - - - - - - - - - - Provides correct transcript products using priority-based cascading logic: - Priority 1: 1:1 Gene:Transcript + Preferred Curated GeneFeatureProduct (is_preferred=1, Sanger|VEuPathDB|Apollo) - Priority 2: 1:1 Gene:Transcript + Any Curated GeneFeatureProduct (Sanger|VEuPathDB|Apollo) - Priority 3: Preferred Curated TranscriptProduct (is_preferred=1, Sanger|VEuPathDB|Apollo) - Priority 4: Any Curated TranscriptProduct (Sanger|VEuPathDB|Apollo) - Priority 5: 1:1 Gene:Transcript + All GeneFeatureProduct (concatenated) - Priority 6: All TranscriptProduct (concatenated) - Priority 7: 1:1 Gene:Transcript + GeneFeature.product - Priority 8: Transcript.product (base field) - This is a global table (all organisms) - source_id is globally unique. - - - - - - - - - - - - - - - - @@ -2225,13 +1872,17 @@ create index Organism_projectId_idx&1 ON OrganismAttributes&1 (project_id, sourc One profile per gene per dataset. Used for graphs. + + + + + + @@ -2239,6 +1890,8 @@ create index Organism_projectId_idx&1 ON OrganismAttributes&1 (project_id, sourc + + @@ -2464,6 +2117,146 @@ create index Organism_projectId_idx&1 ON OrganismAttributes&1 (project_id, sourc AND d.external_database_id = r.external_database_id AND profile.node_set_id = ps.node_set_id AND ps.external_database_release_id = r.external_database_release_id + UNION ALL + -- SubjectResult profiles + SELECT + ds.name as dataset_name, ds.type as dataset_type, coalesce(o.abbrev, 'no_org_abbrev') as org_abbrev, + ds.subtype as dataset_subtype, 'values' AS profile_type, ps.node_type, + sr.subject as source_id, sr.node_set_id as profile_study_id, + ps.name as profile_set_name, + null as profile_set_suffix, + CASE WHEN replace(sr.profile_as_string, 'NA' || CHR(9), '') = 'NA' THEN null ELSE sr.profile_as_string END as profile_as_string, + '-1' as max_value, '1' as min_value, '-1' as max_timepoint, '-1' as min_timepoint + FROM apidb.DataSource ds + JOIN sres.ExternalDatabase d ON ds.name = d.name + JOIN sres.ExternalDatabaseRelease r ON ds.version = r.version + AND d.external_database_id = r.external_database_id + LEFT JOIN apidb.organism o ON ds.taxon_id = o.taxon_id + JOIN study.NodeSet ps ON ps.external_database_release_id = r.external_database_release_id + JOIN (SELECT sl.node_set_id, result.subject, + string_agg(coalesce(round(result.value::numeric, 2)::varchar, 'NA'), chr(9) order by pan.node_order_num) as profile_as_string + FROM study.ProtocolAppNode pan, NodeSetOutputNode sl, apidb.SubjectResult result + WHERE result.protocol_app_node_id = sl.protocol_app_node_id + AND result.protocol_app_node_id = pan.protocol_app_node_id + GROUP BY sl.node_set_id, result.subject + ) sr ON sr.node_set_id = ps.node_set_id + UNION ALL + -- OntologyTermResult profiles + SELECT + ds.name as dataset_name, ds.type as dataset_type, coalesce(o.abbrev, 'no_org_abbrev') as org_abbrev, + ds.subtype as dataset_subtype, 'value' AS profile_type, ps.node_type, + otr.term_name as source_id, otr.node_set_id as profile_study_id, + ps.name as profile_set_name, + null as profile_set_suffix, + CASE WHEN replace(otr.profile_as_string, 'NA' || CHR(9), '') = 'NA' THEN null ELSE otr.profile_as_string END as profile_as_string, + '-1' as max_value, '1' as min_value, '-1' as max_timepoint, '-1' as min_timepoint + FROM apidb.DataSource ds + JOIN sres.ExternalDatabase d ON ds.name = d.name + JOIN sres.ExternalDatabaseRelease r ON ds.version = r.version + AND d.external_database_id = r.external_database_id + LEFT JOIN apidb.organism o ON ds.taxon_id = o.taxon_id + JOIN study.NodeSet ps ON ps.external_database_release_id = r.external_database_release_id + JOIN (SELECT sl.node_set_id, ot.name as term_name, + string_agg(coalesce(round(result.value::numeric, 2)::varchar, 'NA'), chr(9) order by pan.node_order_num) as profile_as_string + FROM study.ProtocolAppNode pan, NodeSetOutputNode sl, + apidb.OntologyTermResult result, sres.OntologyTerm ot + WHERE ot.ontology_term_id = result.ontology_term_id + AND result.protocol_app_node_id = sl.protocol_app_node_id + AND result.protocol_app_node_id = pan.protocol_app_node_id + GROUP BY sl.node_set_id, ot.name + ) otr ON otr.node_set_id = ps.node_set_id + UNION ALL + -- Compound profiles from results.CompoundMassSpec (values with isotopomers) + SELECT + ds.name as dataset_name, ds.type as dataset_type, coalesce(o.abbrev, 'no_org_abbrev') as org_abbrev, + ds.subtype as dataset_subtype, 'values' AS profile_type, ps.node_type, + CASE WHEN cp.isotopomer IS NOT NULL THEN ca.source_id || '|' || cp.isotopomer + ELSE ca.source_id + END as source_id, + cp.node_set_id as profile_study_id, + ps.name as profile_set_name, + null as profile_set_suffix, + CASE WHEN replace(cp.profile_as_string, 'NA' || CHR(9), '') = 'NA' THEN null ELSE cp.profile_as_string END as profile_as_string, + '-1' as max_value, '1' as min_value, '-1' as max_timepoint, '-1' as min_timepoint + FROM apidb.DataSource ds + JOIN sres.ExternalDatabase d ON ds.name = d.name + JOIN sres.ExternalDatabaseRelease r ON ds.version = r.version + AND d.external_database_id = r.external_database_id + LEFT JOIN apidb.organism o ON ds.taxon_id = o.taxon_id + JOIN study.NodeSet ps ON ps.external_database_release_id = r.external_database_release_id + JOIN (SELECT sl.node_set_id, result.compound_id, result.isotopomer, + string_agg(coalesce(round(result.value::numeric, 2)::varchar, 'NA'), chr(9) order by pan.node_order_num) as profile_as_string + FROM study.ProtocolAppNode pan, NodeSetOutputNode sl, + (SELECT max(value) as value, compound_id, protocol_app_node_id, isotopomer + FROM results.CompoundMassSpec + GROUP BY compound_id, protocol_app_node_id, isotopomer) result + WHERE result.protocol_app_node_id = sl.protocol_app_node_id + AND result.protocol_app_node_id = pan.protocol_app_node_id + GROUP BY sl.node_set_id, result.compound_id, result.isotopomer + ) cp ON cp.node_set_id = ps.node_set_id + JOIN webready.CompoundAttributes ca ON ca.id = cp.compound_id + UNION ALL + -- Compound profiles from apidb.CompoundMassSpecResult (values) + SELECT + ds.name as dataset_name, ds.type as dataset_type, coalesce(o.abbrev, 'no_org_abbrev') as org_abbrev, + ds.subtype as dataset_subtype, 'values' AS profile_type, ps.node_type, + CASE WHEN cpc.isotopomer IS NOT NULL THEN ca.source_id || '|' || cpc.isotopomer + WHEN cph.mass IS NOT NULL THEN ca.source_id || '|' || cph.mass || '|' || cph.retention_time + ELSE ca.source_id + END as source_id, + cmsr_agg.node_set_id as profile_study_id, + ps.name as profile_set_name, + null as profile_set_suffix, + CASE WHEN replace(cmsr_agg.profile_as_string, 'NA' || CHR(9), '') = 'NA' THEN null ELSE cmsr_agg.profile_as_string END as profile_as_string, + '-1' as max_value, '1' as min_value, '-1' as max_timepoint, '-1' as min_timepoint + FROM apidb.DataSource ds + JOIN sres.ExternalDatabase d ON ds.name = d.name + JOIN sres.ExternalDatabaseRelease r ON ds.version = r.version + AND d.external_database_id = r.external_database_id + LEFT JOIN apidb.organism o ON ds.taxon_id = o.taxon_id + JOIN study.NodeSet ps ON ps.external_database_release_id = r.external_database_release_id + JOIN (SELECT sl.node_set_id, cmsr.compound_peaks_id, + string_agg(coalesce(round(cmsr.value::numeric, 2)::varchar, 'NA'), chr(9) order by pan.node_order_num) as profile_as_string + FROM study.ProtocolAppNode pan, NodeSetOutputNode sl, apidb.CompoundMassSpecResult cmsr + WHERE cmsr.protocol_app_node_id = sl.protocol_app_node_id + AND cmsr.protocol_app_node_id = pan.protocol_app_node_id + AND pan.name like '%mean%' + GROUP BY sl.node_set_id, cmsr.compound_peaks_id + ) cmsr_agg ON cmsr_agg.node_set_id = ps.node_set_id + JOIN apidb.CompoundPeaksChebi cpc ON cpc.compound_peaks_id = cmsr_agg.compound_peaks_id + JOIN apidb.CompoundPeaks cph ON cph.compound_peaks_id = cpc.compound_peaks_id + JOIN webready.CompoundAttributes ca ON ca.id = cpc.compound_id + UNION ALL + -- Compound profiles from apidb.CompoundMassSpecResult (percentiles) + SELECT + ds.name as dataset_name, ds.type as dataset_type, coalesce(o.abbrev, 'no_org_abbrev') as org_abbrev, + ds.subtype as dataset_subtype, 'percentiles' AS profile_type, ps.node_type, + CASE WHEN cpc.isotopomer IS NOT NULL THEN ca.source_id || '|' || cpc.isotopomer + WHEN cph.mass IS NOT NULL THEN ca.source_id || '|' || cph.mass || '|' || cph.retention_time + ELSE ca.source_id + END as source_id, + cmsr_agg.node_set_id as profile_study_id, + ps.name as profile_set_name, + null as profile_set_suffix, + CASE WHEN replace(cmsr_agg.profile_as_string, 'NA' || CHR(9), '') = 'NA' THEN null ELSE cmsr_agg.profile_as_string END as profile_as_string, + '-1' as max_value, '1' as min_value, '-1' as max_timepoint, '-1' as min_timepoint + FROM apidb.DataSource ds + JOIN sres.ExternalDatabase d ON ds.name = d.name + JOIN sres.ExternalDatabaseRelease r ON ds.version = r.version + AND d.external_database_id = r.external_database_id + LEFT JOIN apidb.organism o ON ds.taxon_id = o.taxon_id + JOIN study.NodeSet ps ON ps.external_database_release_id = r.external_database_release_id + JOIN (SELECT sl.node_set_id, cmsr.compound_peaks_id, + string_agg(coalesce(round(cmsr.percentile::numeric, 2)::varchar, 'NA'), chr(9) order by pan.node_order_num) as profile_as_string + FROM study.ProtocolAppNode pan, NodeSetOutputNode sl, apidb.CompoundMassSpecResult cmsr + WHERE cmsr.protocol_app_node_id = sl.protocol_app_node_id + AND cmsr.protocol_app_node_id = pan.protocol_app_node_id + AND pan.name like '%mean%' + GROUP BY sl.node_set_id, cmsr.compound_peaks_id + ) cmsr_agg ON cmsr_agg.node_set_id = ps.node_set_id + JOIN apidb.CompoundPeaksChebi cpc ON cpc.compound_peaks_id = cmsr_agg.compound_peaks_id + JOIN apidb.CompoundPeaks cph ON cph.compound_peaks_id = cpc.compound_peaks_id + JOIN webready.CompoundAttributes ca ON ca.id = cpc.compound_id ]]> @@ -2496,6 +2289,14 @@ create index Organism_projectId_idx&1 ON OrganismAttributes&1 (project_id, sourc ]]> + + + +