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0521210
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Fix srf2named_fastq to output the proper /2 in paired end reads
author
Diane Trout
<diane@caltech.edu>
Tue, 22 Jun 2010 19:07:48 +0000
(19:07 +0000)
committer
Diane Trout
<diane@caltech.edu>
Tue, 22 Jun 2010 19:07:48 +0000
(19:07 +0000)
scripts/srf2named_fastq.py
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diff --git
a/scripts/srf2named_fastq.py
b/scripts/srf2named_fastq.py
index b6b8b55cc82b5c929c51293a7497bedd91883db4..22edc12743b52f1f6b9141cdf566bc1fe28e4f19 100755
(executable)
--- a/
scripts/srf2named_fastq.py
+++ b/
scripts/srf2named_fastq.py
@@
-1,4
+1,5
@@
#!/usr/bin/env python
#!/usr/bin/env python
+import logging
from optparse import OptionParser
import os
from subprocess import Popen, PIPE
from optparse import OptionParser
import os
from subprocess import Popen, PIPE
@@
-14,6
+15,11
@@
def main(cmdline=None):
if len(args) != 1:
parser.error("Requires one argument")
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:
if opts.flowcell is not None:
header = "%s_" % (opts.flowcell,)
else:
@@
-58,6
+64,8
@@
You can also force the flowcell ID to be added to the header.""")
help='actual sequence mid point')
parser.add_option('-s','--single', default=None,
help="single fastq target name")
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
return parser
@@
-70,7
+78,8
@@
def srf_open(filename, cnf1=False):
if cnf1:
cmd.append('-c')
cmd.append(filename)
if cnf1:
cmd.append('-c')
cmd.append(filename)
-
+
+ logging.info('srf command: %s' % (" ".join(cmd),))
p = Popen(cmd, stdout=PIPE)
return p.stdout
p = Popen(cmd, stdout=PIPE)
return p.stdout
@@
-109,7
+118,7
@@
def convert_single_to_two_fastq(instream, target1, target2, mid=None, header='')
target2.write('@')
target2.write(header)
target2.write(line[1:])
target2.write('@')
target2.write(header)
target2.write(line[1:])
- target2.write("/
1
")
+ target2.write("/
2
")
target2.write(os.linesep)
# quality header
target2.write(os.linesep)
# quality header