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Commit ec737360 authored by Venkat Malladi's avatar Venkat Malladi
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Defaulted to zcat instead of unzip file.

parent e2f0afca
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1 merge request!18Resolve "Add in current chip-analysis functionality."
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in 7 hours, 23 minutes, and 24 seconds
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workflow/scripts/xcor.py
+ 7
− 7
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...@@ -61,20 +61,20 @@ def xcor(tag, paired): ...@@ -61,20 +61,20 @@ def xcor(tag, paired):
'''Use spp to calculate cross-correlation stats.''' '''Use spp to calculate cross-correlation stats.'''
tag_basename = os.path.basename(utils.strip_extensions(tag, ['.gz'])) tag_basename = os.path.basename(utils.strip_extensions(tag, ['.gz']))
uncompressed_tag_filename = tag_basename uncompressed_tag_filename = tag_basename
out, err = utils.run_pipe([
'gzip -dc %s > ' % (tag)], outfile=uncompressed_tag_filename)
# Subsample tagAlign file # Subsample tagAlign file
NREADS = 15000000 NREADS = 15000000
subsampled_tag_filename = \ subsampled_tag_filename = \
tag_basename + ".%d.tagAlign.gz" % (NREADS/1000000) tag_basename + ".%d.tagAlign.gz" % (NREADS/1000000)
steps = [ steps = [
'grep -v "chrM" %s' % (uncompressed_tag_filename), 'zcat %s' % (tag),
'shuf -n %d --random-source=%s' % (NREADS, uncompressed_tag_filename) 'grep -v "chrM"',
] 'shuf -n %d --random-source=%s' % (NREADS, tag)]
if paired: if paired:
steps.extend([r"""awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}'"""]) steps.extend([r"""awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}'"""])
......
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