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ef361ca
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Add a method to override command used to convert srf to fastq files.
author
Diane Trout
<diane@caltech.edu>
Tue, 22 Nov 2011 22:13:23 +0000
(14:13 -0800)
committer
Diane Trout
<diane@caltech.edu>
Tue, 22 Nov 2011 22:13:23 +0000
(14:13 -0800)
htsworkflow/pipelines/srf2fastq.py
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diff --git
a/htsworkflow/pipelines/srf2fastq.py
b/htsworkflow/pipelines/srf2fastq.py
index 61f93c77fe892af71ea5a130ced53e0f12a2b530..c73bb2cc3f93953de73210a751dfd9f463c8b832 100755
(executable)
--- a/
htsworkflow/pipelines/srf2fastq.py
+++ b/
htsworkflow/pipelines/srf2fastq.py
@@
-46,7
+46,7
@@
def main(cmdline=None):
# open the srf, fastq, or compressed fastq
if is_srf(args[0]):
# open the srf, fastq, or compressed fastq
if is_srf(args[0]):
- source = srf_open(args[0], opts.cnf1)
+ source = srf_open(args[0], opts.
srf2fastq, opts.
cnf1)
else:
source = autoopen(args[0])
else:
source = autoopen(args[0])
@@
-81,14
+81,18
@@
You can also force the flowcell ID to be added to the header.""")
help="Report software version")
parser.add_option('--cnf1', default=False, action="store_true",
help="Force cnf1 mode in srf2fastq")
help="Report software version")
parser.add_option('--cnf1', default=False, action="store_true",
help="Force cnf1 mode in srf2fastq")
+ parser.add_option('--srf2fastq', default='srf2fastq',
+ help='specify srf2fastq command')
return parser
return parser
-def srf_open(filename, cnf1=False):
+def srf_open(filename,
srf2fastq_cmd,
cnf1=False):
"""
Make a stream from srf file using srf2fastq
"""
"""
Make a stream from srf file using srf2fastq
"""
- cmd = ['srf2fastq']
+ if not os.path.exists(srf2fastq_cmd):
+ LOGGER.error("srf command: %s doesn't exist" % (srf2fastq_cmd,))
+ cmd = [srf2fastq_cmd]
if cnf1 or is_cnf1(filename):
cmd.append('-c')
cmd.append(filename)
if cnf1 or is_cnf1(filename):
cmd.append('-c')
cmd.append(filename)