# 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])
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)