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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 = 'velvetg_wrapper.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 contigs = sys.argv[2]
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29 stats = sys.argv[3]
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30 LastGraph = sys.argv[4]
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31 afgFile = sys.argv[5]
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32 unusedReadsFile = sys.argv[6]
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33 inputs = string.join(sys.argv[7:],' ')
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34 cmdline = 'velvetg %s %s > /dev/null' % (working_dir, inputs)
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35 # print >> sys.stderr, cmdline # so will appear as blurb for file
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36 try:
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37 proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE )
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38 returncode = proc.wait()
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39 # get stderr, allowing for case where it's very large
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40 stderr = ''
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41 buffsize = 1048576
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42 try:
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43 while True:
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44 stderr += proc.stderr.read( buffsize )
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45 if not stderr or len( stderr ) % buffsize != 0:
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46 break
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47 except OverflowError:
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48 pass
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49 if returncode != 0:
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50 raise Exception, stderr
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51 except Exception, e:
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52 stop_err( 'Error running velvetg ' + str( e ) )
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53 out = open(contigs,'w')
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54 contigs_path = os.path.join(working_dir,'contigs.fa')
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55 for line in open( contigs_path ):
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56 out.write( "%s" % (line) )
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57 out.close()
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58 out = open(stats,'w')
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59 stats_path = os.path.join(working_dir,'stats.txt')
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60 for line in open( stats_path ):
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61 out.write( "%s" % (line) )
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62 out.close()
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63 if LastGraph != 'None':
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64 out = open(LastGraph,'w')
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65 LastGraph_path = os.path.join(working_dir,'LastGraph')
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66 for line in open( LastGraph_path ):
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67 out.write( "%s" % (line) )
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68 out.close()
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69 if afgFile != 'None':
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70 out = open(afgFile,'w')
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71 afgFile_path = os.path.join(working_dir,'velvet_asm.afg')
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72 try:
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73 for line in open( afgFile_path ):
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74 out.write( "%s" % (line) )
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75 except:
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76 logging.warn( 'error reading %s' %(afgFile_path))
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77 pass
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78 out.close()
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79 if unusedReadsFile != 'None':
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80 out = open(unusedReadsFile,'w')
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81 unusedReadsFile_path = os.path.join(working_dir,'UnusedReads.fa')
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82 try:
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83 for line in open( unusedReadsFile_path ):
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84 out.write( "%s" % (line) )
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85 except:
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86 logging.info( 'error reading %s' %(unusedReadsFile_path))
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87 pass
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88 out.close()
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89
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90 if __name__ == "__main__": __main__()
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