[2] | 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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