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Add option to compress fastq file
author
Diane Trout
<diane@ghic.org>
Tue, 18 Feb 2014 23:34:14 +0000
(15:34 -0800)
committer
Diane Trout
<diane@caltech.edu>
Tue, 18 Feb 2014 23:36:17 +0000
(15:36 -0800)
htsworkflow/pipelines/desplit_fastq.py
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diff --git
a/htsworkflow/pipelines/desplit_fastq.py
b/htsworkflow/pipelines/desplit_fastq.py
index 2ad853c1fe2053f91ffaf19268264b159798e520..83a995588079f34088e5b07ac7d098bfb08b3072 100644
(file)
--- a/
htsworkflow/pipelines/desplit_fastq.py
+++ b/
htsworkflow/pipelines/desplit_fastq.py
@@
-1,7
+1,8
@@
#!/usr/bin/env python
"""Write fastq data from multiple compressed files into a single file
"""
#!/usr/bin/env python
"""Write fastq data from multiple compressed files into a single file
"""
-
+import bz2
+import gzip
from glob import glob
import os
from optparse import OptionParser
from glob import glob
import os
from optparse import OptionParser
@@
-29,7
+30,12
@@
def main(cmdline=None):
return 0
if opts.output is not None:
return 0
if opts.output is not None:
- output = open(opts.output, 'w')
+ if opts.bzip:
+ output = bz2.BZ2File(opts.output,'w')
+ elif opts.gzip:
+ output = gzip.GzipFile(opts.output, 'w')
+ else:
+ output = open(opts.output, 'w')
else:
output = sys.stdout
else:
output = sys.stdout
@@
-51,6
+57,10
@@
def make_parser():
parser.add_option('-s', '--slice',
help="specify python slice, e.g. 0:75, 0:-1",
default=None)
parser.add_option('-s', '--slice',
help="specify python slice, e.g. 0:75, 0:-1",
default=None)
+ parser.add_option('--gzip', default=False, action='store_true',
+ help='gzip output')
+ parser.add_option('--bzip', default=False, action='store_true',
+ help='bzip output')
parser.add_option("--version", default=False, action="store_true",
help="report software version")
return parser
parser.add_option("--version", default=False, action="store_true",
help="report software version")
return parser