return 0
if opts.output is not None:
- if opts.bzip:
- output = bz2.open(opts.output, 'wt')
- elif opts.gzip:
- output = gzip.open(opts.output, 'wt')
- else:
- output = open(opts.output, 'w')
+ output = open_output(opts.output, opts)
else:
output = sys.stdout
return parser
+def open_output(output, opts):
+ """Open output file with right compression library
+ """
+ if opts.bzip:
+ return bz2.open(output, 'wt')
+ elif opts.gzip:
+ return gzip.open(output, 'wt')
+ else:
+ return open(output, 'w')
+
+
def file_generator(pattern_list):
"""Given a list of glob patterns return decompressed streams
"""
from htsworkflow.util.version import version
from htsworkflow.util.conversion import parse_slice
+from htsworkflow.pipelines.desplit_fastq import open_output
def main(cmdline=None):
qseq_generator = [sys.stdin]
if opts.output is not None:
- output = open(opts.output, 'w')
+ output = open_output(opts.output, opts)
else:
output = sys.stdout
if opts.nopass_output is not None:
- nopass_output = open(opts.nopass_output, 'w')
+ nopass_output = open_output(opts.nopass_output, opts)
else:
nopass_output = None
default=None)
parser.add_option("--pf", help="report pass filter flag", default=False,
action="store_true")
+ 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")
for source in sources:
paths.append(source.path)
paths.sort()
+ compression_argument = self.format_compression_flag()
+
return {
'pyscript': qseq2fastq.__file__,
'flowcell': sources[0].flowcell_id,
'target': target_pathname,
+ 'compression': compression_argument,
'sources': paths,
'ispaired': sources[0].ispaired,
'istar': len(sources) == 1,
for source in sources:
paths.append(source.path)
paths.sort()
- compression_argument = ''
- if self.compression:
- compression_argument = '--'+self.compression
+ compression_argument = self.format_compression_flag()
return {
'pyscript': desplit_fastq.__file__,
'ispaired': sources[0].ispaired,
}
+ def format_compression_flag(self):
+ return '--'+self.compression if self.compression else ''
+
def make_lane_dict(lib_db, lib_id):
"""