From 264ecc132ec008a35d8fcbd569432643d3839678 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Tue, 22 Nov 2011 14:13:23 -0800 Subject: [PATCH] Add a method to override command used to convert srf to fastq files. --- htsworkflow/pipelines/srf2fastq.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/htsworkflow/pipelines/srf2fastq.py b/htsworkflow/pipelines/srf2fastq.py index 61f93c7..c73bb2c 100755 --- 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]): - source = srf_open(args[0], opts.cnf1) + source = srf_open(args[0], opts.srf2fastq, opts.cnf1) 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") + parser.add_option('--srf2fastq', default='srf2fastq', + help='specify srf2fastq command') return parser -def srf_open(filename, cnf1=False): +def srf_open(filename, srf2fastq_cmd, cnf1=False): """ 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) -- 2.30.2