Mercurial > repos > konradpaszkiewicz > preppereadsforveletfasta

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