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Fix samtools piping #325

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merged 3 commits into from
Sep 7, 2023
Merged

Fix samtools piping #325

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93ac742
Remove samtools pipe stderr to stdout
Colelyman Aug 11, 2023
c6f8277
Remove extra spacing at end of lines and add missing comma in WGS
Colelyman Aug 11, 2023
caa8531
Log stderr from samtools in CRISPRessoWGS
Colelyman Sep 7, 2023
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32 changes: 18 additions & 14 deletions CRISPResso2/CRISPRessoWGSCORE.py
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Original file line number Diff line number Diff line change
Expand Up @@ -171,14 +171,18 @@ def write_trimmed_fastq(in_bam_filename, bpstart, bpend, out_fastq_filename):
n_reasd (int): number of reads written to the output fastq file
"""
p = sb.Popen(
'samtools view %s | cut -f1,4,6,10,11' % in_bam_filename,
stdout = sb.PIPE,
stderr = sb.STDOUT,
shell=True
)

output=p.communicate()[0].decode('utf-8')
n_reads=0
f'samtools view {in_bam_filename} | cut -f1,4,6,10,11',
stdout=sb.PIPE,
stderr=sb.PIPE,
shell=True,
text=True,
)

output, stderr = p.communicate()
n_reads = 0
if stderr:
logger.debug('Stderr from samtools view:')
logger.debug(stderr)

with gzip.open(out_fastq_filename, 'wt') as outfile:
for line in output.split('\n'):
Expand Down Expand Up @@ -318,13 +322,13 @@ def print_stacktrace_if_debug():
))
sys.exit()

parser = CRISPRessoShared.getCRISPRessoArgParser(parser_title = 'CRISPRessoWGS Parameters', required_params=[],
parser = CRISPRessoShared.getCRISPRessoArgParser(parser_title = 'CRISPRessoWGS Parameters', required_params=[],
suppress_params=['bam_input',
'bam_chr_loc'
'fastq_r1',
'fastq_r2',
'amplicon_seq',
'amplicon_name',
'bam_chr_loc',
'fastq_r1',
'fastq_r2',
'amplicon_seq',
'amplicon_name',
])

#tool specific optional
Expand Down