Mercurial > repos > konradpaszkiewicz > oasesoptimiser
annotate oases_optimiser.py @ 0:53e887dda799 default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | konradpaszkiewicz |
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date | Tue, 07 Jun 2011 17:41:37 -0400 |
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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 VelvetOptimiser Wrapper |
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5 Adapted from velveth and velvetg tools in Galaxy |
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6 Konrad Paszkiewicz University of Exeter, UK. |
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7 |
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8 """ |
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9 import pkg_resources; |
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10 import logging, os, string, sys, tempfile, glob, shutil, types, urllib |
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11 import shlex, subprocess |
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12 from optparse import OptionParser, OptionGroup |
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13 from stat import * |
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14 |
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15 |
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16 log = logging.getLogger( __name__ ) |
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17 |
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18 assert sys.version_info[:2] >= ( 2, 4 ) |
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19 |
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20 def stop_err( msg ): |
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21 sys.stderr.write( "%s\n" % msg ) |
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22 sys.exit() |
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23 |
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24 def __main__(): |
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25 #Parse Command Line |
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26 s = 'oases_optimiser.py: argv = %s\n' % (sys.argv) |
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27 #print >> sys.stderr, s # so will appear as blurb for file |
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28 argcnt = len(sys.argv) |
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29 starthash = sys.argv[1] |
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30 endhash = sys.argv[2] |
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31 inputs = sys.argv[3] |
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32 contigs = sys.argv[4] |
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33 LastGraph = sys.argv[5] |
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34 afgFile = sys.argv[6] |
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35 unused_reads_fasta = sys.argv[7] |
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36 stats = sys.argv[8] |
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37 othervelvetgoptions = sys.argv[9] |
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38 otheroasesoptions = sys.argv[10] |
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39 transcripts = sys.argv[11] |
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40 splicingevents = sys.argv[12] |
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41 contigordering = sys.argv[13] |
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42 #contigs.extra_files_path |
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43 |
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44 |
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45 working_dir = '' |
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46 |
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47 cmdline = '/users/galaxy/galaxyscripts/oases_optimiser.sh %s %s \'%s\' %s %s 2&1>/dev/null' % (starthash, endhash, inputs, othervelvetgoptions, otheroasesoptions) |
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48 #print >> sys.stderr, cmdline # so will appear as blurb for file |
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49 try: |
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50 proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE ) |
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51 returncode = proc.wait() |
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52 # get stderr, allowing for case where it's very large |
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53 stderr = '' |
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54 buffsize = 1048576 |
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55 try: |
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56 while True: |
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57 stderr += proc.stderr.read( buffsize ) |
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58 if not stderr or len( stderr ) % buffsize != 0: |
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59 break |
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60 except OverflowError: |
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61 pass |
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62 if returncode != 0: |
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63 raise Exception, stderr |
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64 except Exception, e: |
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65 stop_err( 'Error running oases_optimiser.py' + str( e ) ) |
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66 out = open(transcripts,'w') |
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67 transcript_path = os.path.join(working_dir,'transcripts.fa') |
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68 #print >> sys.stderr, path |
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69 for line in open(transcript_path): |
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70 out.write( "%s" % (line) ) |
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71 out.close() |
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72 |
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73 out = open(splicingevents,'w') |
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74 path = os.path.join(working_dir,'splicing_events.txt') |
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75 #print >> sys.stderr, contigs_path |
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76 for line in open(path ): |
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77 out.write( "%s" % (line) ) |
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78 out.close() |
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79 |
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80 |
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81 |
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82 out = open(contigs,'w') |
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83 contigs_path = os.path.join(working_dir,'contigs.fa') |
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84 #print >> sys.stderr, contigs_path |
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85 for line in open(contigs_path ): |
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86 out.write( "%s" % (line) ) |
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87 out.close() |
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88 out = open(stats,'w') |
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89 stats_path = os.path.join(working_dir,'stats.txt') |
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90 for line in open( stats_path ): |
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91 out.write( "%s" % (line) ) |
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92 out.close() |
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93 if LastGraph != 'None': |
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94 out = open(LastGraph,'w') |
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95 LastGraph_path = os.path.join(working_dir,'LastGraph') |
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96 for line in open( LastGraph_path ): |
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97 out.write( "%s" % (line) ) |
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98 out.close() |
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99 if afgFile != 'None': |
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100 out = open(afgFile,'w') |
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101 afgFile_path = os.path.join(working_dir,'oases_asm.afg') |
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102 try: |
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103 for line in open( afgFile_path ): |
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104 out.write( "%s" % (line) ) |
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105 except: |
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106 logging.warn( 'error reading %s' %(afgFile_path)) |
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107 pass |
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108 out.close() |
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109 if unused_reads_fasta != 'None': |
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110 out = open(unused_reads_fasta,'w') |
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111 unused_reads_fasta_path = os.path.join(working_dir,'UnusedReads.fa') |
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112 try: |
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113 for line in open( unused_reads_fasta_path ): |
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114 out.write( "%s" % (line) ) |
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115 except: |
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116 logging.info( 'error reading %s' %(unused_reads_fasta_path)) |
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117 pass |
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118 out.close() |
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119 |
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120 if __name__ == "__main__": __main__() |