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import os
import subprocess
import pysam
from TestUtils import BAM_DATADIR, force_str
def build_fetch_with_samtoolsshell(fn):
retval = os.popen("samtools view {} 2> /dev/null | wc -l".format(fn)).read()
return int(retval.strip())
def build_fetch_with_samtoolspipe(fn):
FNULL = open(os.devnull, 'w')
with subprocess.Popen(["samtools", "view", fn],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=FNULL) as proc:
return len(proc.stdout.readlines())
def build_fetch_with_pysam(*args, **kwargs):
with pysam.AlignmentFile(*args, **kwargs) as inf:
return len(list(inf.fetch()))
def build_query_sequences_with_samtoolsshell(fn):
retval = os.popen("samtools view {} 2> /dev/null | cut -f 11".format(fn)).read()
return force_str(retval).splitlines()
def build_query_sequences_with_samtoolspipe(fn):
FNULL = open(os.devnull, 'w')
with subprocess.Popen(["samtools", "view", fn],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=FNULL) as proc:
data = [force_str(x).split()[10] for x in proc.stdout.readlines()]
return data
def build_query_sequences_with_pysam(*args, **kwargs):
with pysam.AlignmentFile(*args, **kwargs) as inf:
data = [x.query_sequence for x in inf]
return data
def build_query_qualities_with_pysam(*args, **kwargs):
with pysam.AlignmentFile(*args, **kwargs) as inf:
data = [x.query_qualities for x in inf]
return data
def build_query_sequences_flagfilter_with_samtoolsshell(fn):
retval = os.popen("samtools view -f 2 {} 2> /dev/null | cut -f 11".format(fn)).read()
return force_str(retval).splitlines()
def build_query_sequences_flagfilter_with_samtoolspipe(fn):
FNULL = open(os.devnull, 'w')
with subprocess.Popen(["samtools", "view", "-f", "2", fn],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=FNULL) as proc:
data = [force_str(x).split()[10] for x in proc.stdout.readlines()]
return data
def build_query_sequences_flagfilter_with_pysam(*args, **kwargs):
with pysam.AlignmentFile(*args, **kwargs) as inf:
data = [x.query_sequence for x in inf if x.is_proper_pair]
return data
def build_query_sequences_directflagfilter_with_pysam(*args, **kwargs):
with pysam.AlignmentFile(*args, **kwargs) as inf:
data = [x.query_sequence for x in inf if x.flag & 2]
return data
def build_aligned_pairs_with_pysam(*args, **kwargs):
matches_only = kwargs.pop("matches_only", False)
with_seq = kwargs.pop("with_seq", False)
with pysam.AlignmentFile(*args, **kwargs) as inf:
data = [x.get_aligned_pairs(matches_only=matches_only, with_seq=with_seq)
for x in inf if not x.is_unmapped]
return data
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