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provide more options for picking how much logging info to spew
author
Diane Trout
<diane@caltech.edu>
Wed, 18 Mar 2009 18:35:49 +0000
(18:35 +0000)
committer
Diane Trout
<diane@caltech.edu>
Wed, 18 Mar 2009 18:35:49 +0000
(18:35 +0000)
scripts/srf
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diff --git
a/scripts/srf
b/scripts/srf
index 9e0fff8de22fd6fd68bc2680f7af97cdee5d8980..4f487ea9d1106e30804fda38576b0431a6160c2b 100644
(file)
--- a/
scripts/srf
+++ b/
scripts/srf
@@
-30,11
+30,15
@@
def make_commands(run_name, lanes, site_name, destdir):
dest_path = os.path.join(destdir, destname)
seq_pattern = 's_%d_*_seq.txt' % (lane,)
dest_path = os.path.join(destdir, destname)
seq_pattern = 's_%d_*_seq.txt' % (lane,)
- cmd = ['solexa2srf',
- '-N', name_prefix,
- '-n', '%3x:%3y',
- '-o', dest_path,
- seq_pattern]
+ #cmd = ['solexa2srf',
+ # '-N', name_prefix,
+ # '-n', '%3x:%3y',
+ # '-o', dest_path,
+ # seq_pattern]
+ cmd = ['illumina2srf',
+ '-v1.0',
+ '-o', dest_path,
+ seq_pattern]
cmd_list.append(" ".join(cmd))
return cmd_list
cmd_list.append(" ".join(cmd))
return cmd_list
@@
-72,7
+76,13
@@
def make_parser():
parser.add_option('-j', '--jobs', default=1, type='int',
help='how many jobs to run simultaneously')
parser.add_option('-j', '--jobs', default=1, type='int',
help='how many jobs to run simultaneously')
-
+ parser.add_option('-v', '--verbose', dest='verbose',
+ default=False, action='store_true',
+ help='report more about internals (INFO)')
+ parser.add_option('--debug', dest='debug',
+ default=False, action='store_true',
+ help='report even more about internals (DEBUG)')
+
return parser
def parse_lane_arg(lane_arg):
return parser
def parse_lane_arg(lane_arg):
@@
-93,7
+103,14
@@
def parse_lane_arg(lane_arg):
def main(cmdline=None):
parser = make_parser()
opts, args = parser.parse_args(cmdline)
def main(cmdline=None):
parser = make_parser()
opts, args = parser.parse_args(cmdline)
-
+
+ if opts.debug:
+ logging.basicConfig(level=logging.DEBUG)
+ elif opts.verbose:
+ logging.basicConfig(level=logging.INFO)
+ else:
+ logging.basicConfig(level=logging.WARNING)
+
if len(args) == 0:
parser.error('need runfolder arguments')
if len(args) == 0:
parser.error('need runfolder arguments')
@@
-145,5
+162,4
@@
def main(cmdline=None):
return 0
if __name__ == "__main__":
return 0
if __name__ == "__main__":
- logging.basicConfig(level=logging.DEBUG)
sys.exit(main(sys.argv[1:]))
sys.exit(main(sys.argv[1:]))