From: Diane Trout <diane@caltech.edu>
Date: Tue, 22 Nov 2011 22:13:23 +0000 (-0800)
Subject: Add a method to override command used to convert srf to fastq files.
X-Git-Tag: v0.5.5~78
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=264ecc132ec008a35d8fcbd569432643d3839678

Add a method to override command used to convert srf to fastq files.
---

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)