From 3fede36522514b41753f0cb9d034110ec259c905 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Tue, 18 Feb 2014 15:34:14 -0800 Subject: [PATCH] Add option to compress fastq file --- htsworkflow/pipelines/desplit_fastq.py | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/htsworkflow/pipelines/desplit_fastq.py b/htsworkflow/pipelines/desplit_fastq.py index 2ad853c..83a9955 100644 --- 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 """ - +import bz2 +import gzip 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: - 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 @@ -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('--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 -- 2.30.2