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Half of #154 fixed
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No longer using global simplenamespace to pass around arguments in trf.
GRM will need more testing to ensure BwaAligner is fine being initialized per-thread.
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@ACEnglish
ACEnglish committed May 12, 2023
1 parent 1d6e48d commit f9f3630
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Showing 3 changed files with 23 additions and 28 deletions.
2 changes: 1 addition & 1 deletion .pylintrc
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Original file line number Diff line number Diff line change
Expand Up @@ -324,4 +324,4 @@ exclude-protected=_asdict,_fields,_replace,_source,_make

# Exceptions that will emit a warning when being caught. Defaults to
# "Exception"
overgeneral-exceptions=Exception
overgeneral-exceptions=builtins.Exception
45 changes: 20 additions & 25 deletions truvari/annotations/trf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,20 +7,17 @@
import sys
import json
import math
import types
import shutil
import logging
import argparse
import functools
import multiprocessing
from io import StringIO
from functools import cmp_to_key

import pysam
import tabix
import truvari

trfshared = types.SimpleNamespace()

try:
from setproctitle import setproctitle # pylint: disable=import-error,useless-suppression
except ModuleNotFoundError:
Expand Down Expand Up @@ -50,7 +47,7 @@ def compare_scores(a, b):
elif aspan < bspan:
ret = -1
return ret
score_sorter = cmp_to_key(compare_scores)
score_sorter = functools.cmp_to_key(compare_scores)

class TRFAnno():
"""
Expand Down Expand Up @@ -344,7 +341,7 @@ def build_from_top(self):
self.tanno = TRFAnno(cur_anno, ref_seq, self.motif_sim)


def process_ref_region(region):
def process_ref_region(region, args):
"""
Process a section of the reference.
Tries to run TRF only once
Expand All @@ -355,7 +352,7 @@ def process_ref_region(region):
logging.debug(f"Starting region {region['chrom']}:{region['start']}-{region['end']}")
setproctitle(f"trf {region['chrom']}:{region['start']}-{region['end']}")

vcf = pysam.VariantFile(trfshared.args.input)
vcf = pysam.VariantFile(args.input)
new_header = edit_header(vcf.header)
out = StringIO()

Expand All @@ -366,10 +363,10 @@ def process_ref_region(region):
return None


m_stack = AnnoStack(list(iter_tr_regions(trfshared.args.repeats,
m_stack = AnnoStack(list(iter_tr_regions(args.repeats,
(region["chrom"], region["start"], region["end"]))),
pysam.FastaFile(trfshared.args.reference),
trfshared.args.motif_similarity)
pysam.FastaFile(args.reference),
args.motif_similarity)

batch = []
fa_fn = truvari.make_temp_filename(suffix=".fa")
Expand All @@ -389,23 +386,23 @@ def process_ref_region(region):

svtype = truvari.entry_variant_type(entry)
svlen = truvari.entry_size(entry)
if svlen < trfshared.args.min_length or svtype not in [truvari.SV.DEL, truvari.SV.INS]:
if svlen < args.min_length or svtype not in [truvari.SV.DEL, truvari.SV.INS]:
out.write(str(edit_entry(entry, None, new_header)))
continue

if svtype == truvari.SV.DEL:
m_anno = m_stack.tanno.del_annotate(entry, svlen)
out.write(str(edit_entry(entry, m_anno, new_header)))
elif svtype == truvari.SV.INS:
m_anno = m_stack.tanno.ins_estimate_anno(entry) if not trfshared.args.no_estimate else None
m_anno = m_stack.tanno.ins_estimate_anno(entry) if not args.no_estimate else None
if m_anno:
out.write(str(edit_entry(entry, m_anno, new_header)))
else:
batch.append((entry, m_stack.tanno))
fa_out.write(f">{len(batch) - 1}\n{m_stack.tanno.make_seq(entry, 'INS')}\n")

if batch:
annotations = run_trf(fa_fn, trfshared.args.executable, trfshared.args.trf_params)
annotations = run_trf(fa_fn, args.executable, args.trf_params)
for key, (entry, tanno) in enumerate(batch):
key = str(key)
m_anno = None
Expand All @@ -420,17 +417,17 @@ def process_ref_region(region):
logging.debug(f"Done region {region['chrom']}:{region['start']}-{region['end']}")
return out.read()

def process_tr_region(region):
def process_tr_region(region, args):
"""
Process vcf lines from a tr reference section
"""
logging.debug(f"Starting region {region['chrom']}:{region['start']}-{region['end']}")
setproctitle(f"trf {region['chrom']}:{region['start']}-{region['end']}")

ref = pysam.FastaFile(trfshared.args.reference)
ref = pysam.FastaFile(args.reference)
ref_seq = ref.fetch(region["chrom"], region["start"], region["end"])
tanno = TRFAnno(region, ref_seq, trfshared.args.motif_similarity, trfshared.args.buffer)
vcf = pysam.VariantFile(trfshared.args.input)
tanno = TRFAnno(region, ref_seq, args.motif_similarity, args.buffer)
vcf = pysam.VariantFile(args.input)
new_header = edit_header(vcf.header)
out = StringIO()

Expand All @@ -448,15 +445,15 @@ def process_tr_region(region):
continue
svtype = truvari.entry_variant_type(entry)
svlen = truvari.entry_size(entry)
if svlen < trfshared.args.min_length or svtype not in [truvari.SV.DEL, truvari.SV.INS]:
if svlen < args.min_length or svtype not in [truvari.SV.DEL, truvari.SV.INS]:
out.write(str(edit_entry(entry, None, new_header)))
continue

if svtype == truvari.SV.DEL:
m_anno = tanno.del_annotate(entry, svlen)
out.write(str(edit_entry(entry, m_anno, new_header)))
elif svtype == truvari.SV.INS:
m_anno = tanno.ins_estimate_anno(entry) if not trfshared.args.no_estimate else None
m_anno = tanno.ins_estimate_anno(entry) if not args.no_estimate else None
if m_anno:
out.write(str(edit_entry(entry, m_anno, new_header)))
else:
Expand All @@ -465,7 +462,7 @@ def process_tr_region(region):
fa_out.write(f">{len(batch) - 1}\n{seq}\n")

if batch:
annotations = run_trf(fa_fn, trfshared.args.executable, trfshared.args.trf_params)
annotations = run_trf(fa_fn, args.executable, args.trf_params)
for key, entry in enumerate(batch):
key = str(key)
m_anno = None
Expand Down Expand Up @@ -634,20 +631,18 @@ def trf_main(cmdargs):
""" TRF annotation """
args = parse_args(cmdargs)
check_params(args)
trfshared.args = args

m_regions = None
m_process = None
if args.regions_only:
m_regions = iter_tr_regions(args.repeats)
m_process = process_tr_region
m_process = functools.partial(process_tr_region, args=args)
else:
# refactor. need streaming mode
m_regions = truvari.ref_ranges(args.reference, chunk_size=int(args.chunk_size * 1e6))
m_process = process_ref_region

m_process = functools.partial(process_ref_region, args=args)

vcf = pysam.VariantFile(trfshared.args.input)
vcf = pysam.VariantFile(args.input)
new_header = edit_header(vcf.header)

with multiprocessing.Pool(args.threads, maxtasksperchild=1) as pool:
Expand Down
4 changes: 2 additions & 2 deletions truvari/refine.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -115,8 +115,8 @@ def make_region_report(data):
Given a refine counts DataFrame, calculate the performance of
PPV, TNR, etc. Also adds 'state' column to regions inplace
"""
false_pos = (data['out_fp'] != 0)
false_neg = (data['out_fn'] != 0)
false_pos = data['out_fp'] != 0
false_neg = data['out_fn'] != 0
any_false = false_pos | false_neg

true_positives = (data['out_tp'] != 0) & (data['out_tpbase'] != 0) & ~any_false
Expand Down

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