Mercurial > repos > konradpaszkiewicz > preppereadsforveletfasta
comparison preppereads.py @ 0:4d237a31970b default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
| author | konradpaszkiewicz |
|---|---|
| date | Tue, 07 Jun 2011 17:42:21 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:4d237a31970b |
|---|---|
| 1 #!/usr/bin/env python | |
| 2 | |
| 3 """ | |
| 4 Classes encapsulating decypher tool. | |
| 5 James E Johnson - University of Minnesota | |
| 6 """ | |
| 7 import pkg_resources; | |
| 8 import logging, os, string, sys, tempfile, glob, shutil, types, urllib | |
| 9 import shlex, subprocess | |
| 10 from optparse import OptionParser, OptionGroup | |
| 11 from stat import * | |
| 12 | |
| 13 | |
| 14 log = logging.getLogger( __name__ ) | |
| 15 | |
| 16 assert sys.version_info[:2] >= ( 2, 4 ) | |
| 17 | |
| 18 def stop_err( msg ): | |
| 19 sys.stderr.write( "%s\n" % msg ) | |
| 20 sys.exit() | |
| 21 | |
| 22 def __main__(): | |
| 23 #Parse Command Line | |
| 24 s = 'preppereads.py: argv = %s\n' % (sys.argv) | |
| 25 # print >> sys.stderr, s # so will appear as blurb for file | |
| 26 argcnt = len(sys.argv) | |
| 27 working_dir = sys.argv[1] | |
| 28 input1 = sys.argv[2] | |
| 29 input2 = sys.argv[3] | |
| 30 outpe = sys.argv[4] | |
| 31 outsingletons = sys.argv[5] | |
| 32 cmdline = '/users/galaxy/galaxyscripts/prepare_pe_reads_for_velvet.sh %s %s %s %s %s %s > /dev/null' % (input1, '1.fastq', input2, '2.fastq', 'single.fq', 'pe.fq') | |
| 33 #print >> sys.stderr, cmdline # so will appear as blurb for file | |
| 34 try: | |
| 35 proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE ) | |
| 36 returncode = proc.wait() | |
| 37 # get stderr, allowing for case where it's very large | |
| 38 stderr = '' | |
| 39 buffsize = 1048576 | |
| 40 try: | |
| 41 while True: | |
| 42 stderr += proc.stderr.read( buffsize ) | |
| 43 if not stderr or len( stderr ) % buffsize != 0: | |
| 44 break | |
| 45 except OverflowError: | |
| 46 pass | |
| 47 if returncode != 0: | |
| 48 raise Exception, stderr | |
| 49 except Exception, e: | |
| 50 stop_err( 'Error running preppereads.sh ' + str( e ) ) | |
| 51 | |
| 52 out = open(outpe,'w') | |
| 53 #outpe_path = os.path.join(working_dir,'') | |
| 54 for line in open('pe.fq'): | |
| 55 out.write( "%s" % (line) ) | |
| 56 out.close() | |
| 57 | |
| 58 out = open(outsingletons,'w') | |
| 59 #singletons_path = os.path.join(working_dir,'') | |
| 60 for line in open('single.fq'): | |
| 61 out.write( "%s" % (line) ) | |
| 62 out.close() | |
| 63 | |
| 64 if __name__ == "__main__": __main__() |