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Outliers families #10

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Merged
tlemane merged 4 commits into from
Oct 21, 2026
Merged

Outliers families #10

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c65417e
fix(profile): fix extreme coverage (wip)
tlemane Sep 30, 2026
213dee4
fix(profile): use poisson deviance (wip)
tlemane Oct 1, 2026
3e4f33e
feat(profile): output species detection scores
tlemane Oct 1, 2026
3736ee2
fix(core): batch signature threading
tlemane Oct 21, 2026
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12 changes: 12 additions & 0 deletions metapang/app/profile/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -255,6 +255,18 @@ def gather_candidates():
candidates.append(species)
mp_log.trace(f" candidate species '{species}' (from genome '{name}')")

detection_file = output_directory / f"{sample_name}.detection.tsv"
with open(detection_file, "w") as det:
det.write("genome\tspecies\tf_query\tf_match\tcum_f_query\n")
cum = 0.0
for name, f_query, f_match in gather_results:
cum += float(f_query)
det.write(
f"{name}\t{name.split('@')[0]}\t"
f"{float(f_query):.6f}\t{float(f_match):.6f}\t{cum:.6f}\n"
)
mp_log.info(f"Wrote species detection scores to '{detection_file.name}'")

if candidates:
mp_log.info(f"{len(candidates)} candidate species: {', '.join(candidates)}")
else:
Expand Down
197 changes: 129 additions & 68 deletions metapang/core/index/index.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
import json
import os
import signal
import threading
from collections.abc import Iterable
from concurrent.futures import ProcessPoolExecutor, as_completed
from dataclasses import asdict, dataclass, field
Expand Down Expand Up @@ -246,27 +247,38 @@ def pangenome_construct(

@staticmethod
def file_batch_signature(
file: "Path | list[Path]",
k: int,
scaled: int,
n: int,
force: bool,
nb_cores: int,
queue_size: int,
batch_size: int,
with_log: bool = True,
) -> SourmashSignature:
"""Compute one Sourmash signature for one or several files, in parallel batches.

Several files (e.g. paired-end or split reads) are folded into a single MinHash,
so the result is one signature for the whole sample.
"""
file, k, scaled, n, force, nb_cores, queue_size, batch_size, with_log=True
):
files = [file] if isinstance(file, (str, Path)) else list(file)

man = MinHashManager(ctx=_MP_CONTEXT)
man.register("MinHash", MinHash)
man.start()
m = man.MinHash(n=n, ksize=k, scaled=scaled) # type: ignore[attr-defined]
result = MinHash(n=n, ksize=k, scaled=scaled)
merge_lock = threading.Lock() # callbacks run in a thread of the main process
errors: list[BaseException] = []

def _merge(fut):
try:
mh = fut.result()
except BaseException as e:
errors.append(e)
return
with merge_lock:
result.merge(mh)

def _iter_sequences():
for f in files:
if is_fastx(f):
for record in Fastx(f):
yield record[1]
else:
with zopen(f, "rb") as file_io:
for record in gb_io.iter(file_io):
yield record.sequence.decode("utf-8")

def _submit(executor, batch):
fut = executor.submit(
IndexBuilder.sequence_batch_minhash, batch, k, n, scaled, force
)
fut.add_done_callback(_merge)

with BoundedProcessPoolExecutor(
queue_size,
Expand All @@ -275,60 +287,109 @@ def file_batch_signature(
initializer=_ignore_sigint,
) as executor:
try:
sequences = []
i = 0
for f in files:
if is_fastx(f):
for record in Fastx(f):
sequences.append(record[1])
i += 1
if i % batch_size == 0:
executor.submit(
IndexBuilder.add_sequences_minhash,
m,
sequences,
k,
n,
scaled,
force,
)
sequences = []
else:
with zopen(f, "rb") as file_io:
for record in gb_io.iter(file_io):
sequences.append(record.sequence.decode("utf-8"))
i += 1
if i % batch_size == 0:
executor.submit(
IndexBuilder.add_sequences_minhash,
m,
sequences,
k,
n,
scaled,
force,
)
sequences = []

if sequences:
executor.submit(
IndexBuilder.add_sequences_minhash,
m,
sequences,
k,
n,
scaled,
force,
)

batch = []
for seq in _iter_sequences():
batch.append(seq)
if len(batch) == batch_size:
_submit(executor, batch)
batch = []
if batch:
_submit(executor, batch)
except KeyboardInterrupt:
mp_log_error(with_log, "Interrupted by user (Ctrl+C)")
executor.shutdown(wait=False)
os._exit(1)

signature = SourmashSignature(m.copy(), name=files[0].stem)
man.shutdown()
return signature
if errors:
raise errors[0]

return SourmashSignature(result, name=Path(files[0]).stem)

# @staticmethod
# def file_batch_signature(
# file: "Path | list[Path]",
# k: int,
# scaled: int,
# n: int,
# force: bool,
# nb_cores: int,
# queue_size: int,
# batch_size: int,
# with_log: bool = True,
# ) -> SourmashSignature:
# """Compute one Sourmash signature for one or several files, in parallel batches.

# Several files (e.g. paired-end or split reads) are folded into a single MinHash,
# so the result is one signature for the whole sample.
# """
# files = [file] if isinstance(file, (str, Path)) else list(file)

# man = MinHashManager(ctx=_MP_CONTEXT)
# man.register("MinHash", MinHash)
# man.start()
# m = man.MinHash(n=n, ksize=k, scaled=scaled) # type: ignore[attr-defined]

# with BoundedProcessPoolExecutor(
# queue_size,
# max_workers=nb_cores,
# mp_context=_MP_CONTEXT,
# initializer=_ignore_sigint,
# ) as executor:
# try:
# sequences = []
# i = 0
# for f in files:
# if is_fastx(f):
# for record in Fastx(f):
# sequences.append(record[1])
# i += 1
# if i % batch_size == 0:
# executor.submit(
# IndexBuilder.add_sequences_minhash,
# m,
# sequences,
# k,
# n,
# scaled,
# force,
# )
# sequences = []
# else:
# with zopen(f, "rb") as file_io:
# for record in gb_io.iter(file_io):
# sequences.append(record.sequence.decode("utf-8"))
# i += 1
# if i % batch_size == 0:
# executor.submit(
# IndexBuilder.add_sequences_minhash,
# m,
# sequences,
# k,
# n,
# scaled,
# force,
# )
# sequences = []

# if sequences:
# executor.submit(
# IndexBuilder.add_sequences_minhash,
# m,
# sequences,
# k,
# n,
# scaled,
# force,
# )

# except KeyboardInterrupt:
# mp_log_error(with_log, "Interrupted by user (Ctrl+C)")
# executor.shutdown(wait=False)
# os._exit(1)

# signature = SourmashSignature(m.copy(), name=files[0].stem)
# man.shutdown()
# return signature

def construct(self, nb_cores: int, with_log: bool = True) -> IndexInfo:
"""Construct and save the index, returning its IndexInfo."""
Expand Down
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