From 5b8b8167df36229e0fd0485c85e33f2b1e2f4fbc Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Tue, 22 Jun 2010 19:07:48 +0000 Subject: [PATCH] Fix srf2named_fastq to output the proper /2 in paired end reads --- scripts/srf2named_fastq.py | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/scripts/srf2named_fastq.py b/scripts/srf2named_fastq.py index b6b8b55..22edc12 100755 --- a/scripts/srf2named_fastq.py +++ b/scripts/srf2named_fastq.py @@ -1,4 +1,5 @@ #!/usr/bin/env python +import logging 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 opts.verbose: + logging.basicConfig(level=logging.INFO) + else: + logging.basicConfig(level=logging.WARN) + 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") + parser.add_option('-v', '--verbose', default=False, action="store_true", + help="show information about what we're doing.") return parser @@ -70,7 +78,8 @@ def srf_open(filename, cnf1=False): if cnf1: cmd.append('-c') cmd.append(filename) - + + logging.info('srf command: %s' % (" ".join(cmd),)) 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("/1") + target2.write("/2") target2.write(os.linesep) # quality header -- 2.30.2