#!/usr/bin/env python
+import logging
from optparse import OptionParser
import os
from subprocess import Popen, PIPE
if len(args) != 1:
parser.error("Requires one argument")
+ if opts.verbose:
+ logging.basicConfig(level=logging.INFO)
+ else:
+ logging.basicConfig(level=logging.WARN)
+
if opts.flowcell is not None:
header = "%s_" % (opts.flowcell,)
else:
help='actual sequence mid point')
parser.add_option('-s','--single', default=None,
help="single fastq target name")
+ parser.add_option('-v', '--verbose', default=False, action="store_true",
+ help="show information about what we're doing.")
return parser
if cnf1:
cmd.append('-c')
cmd.append(filename)
-
+
+ logging.info('srf command: %s' % (" ".join(cmd),))
p = Popen(cmd, stdout=PIPE)
return p.stdout
target2.write('@')
target2.write(header)
target2.write(line[1:])
- target2.write("/1")
+ target2.write("/2")
target2.write(os.linesep)
# quality header