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91 lines
2.9 KiB
Python
91 lines
2.9 KiB
Python
#!/usr/bin/env python
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"""
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Classes encapsulating decypher tool.
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James E Johnson - University of Minnesota
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"""
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import pkg_resources;
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import logging, os, string, sys, tempfile, glob, shutil, types, urllib
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import shlex, subprocess
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from optparse import OptionParser, OptionGroup
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from stat import *
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log = logging.getLogger( __name__ )
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assert sys.version_info[:2] >= ( 2, 4 )
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def stop_err( msg ):
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sys.stderr.write( "%s\n" % msg )
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sys.exit()
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def __main__():
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#Parse Command Line
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s = 'velvetg_wrapper.py: argv = %s\n' % (sys.argv)
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# print >> sys.stderr, s # so will appear as blurb for file
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argcnt = len(sys.argv)
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working_dir = sys.argv[1]
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contigs = sys.argv[2]
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stats = sys.argv[3]
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LastGraph = sys.argv[4]
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afgFile = sys.argv[5]
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unusedReadsFile = sys.argv[6]
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inputs = string.join(sys.argv[7:],' ')
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cmdline = 'velvetg %s %s > /dev/null' % (working_dir, inputs)
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# print >> sys.stderr, cmdline # so will appear as blurb for file
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try:
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proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE )
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returncode = proc.wait()
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# get stderr, allowing for case where it's very large
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stderr = ''
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buffsize = 1048576
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try:
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while True:
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stderr += proc.stderr.read( buffsize )
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if not stderr or len( stderr ) % buffsize != 0:
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break
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except OverflowError:
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pass
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if returncode != 0:
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raise Exception, stderr
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except Exception, e:
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stop_err( 'Error running velvetg ' + str( e ) )
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out = open(contigs,'w')
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contigs_path = os.path.join(working_dir,'contigs.fa')
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for line in open( contigs_path ):
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out.write( "%s" % (line) )
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out.close()
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out = open(stats,'w')
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stats_path = os.path.join(working_dir,'stats.txt')
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for line in open( stats_path ):
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out.write( "%s" % (line) )
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out.close()
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if LastGraph != 'None':
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out = open(LastGraph,'w')
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LastGraph_path = os.path.join(working_dir,'LastGraph')
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for line in open( LastGraph_path ):
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out.write( "%s" % (line) )
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out.close()
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if afgFile != 'None':
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out = open(afgFile,'w')
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afgFile_path = os.path.join(working_dir,'velvet_asm.afg')
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try:
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for line in open( afgFile_path ):
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out.write( "%s" % (line) )
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except:
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logging.warn( 'error reading %s' %(afgFile_path))
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pass
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out.close()
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if unusedReadsFile != 'None':
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out = open(unusedReadsFile,'w')
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unusedReadsFile_path = os.path.join(working_dir,'UnusedReads.fa')
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try:
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for line in open( unusedReadsFile_path ):
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out.write( "%s" % (line) )
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except:
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logging.info( 'error reading %s' %(unusedReadsFile_path))
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pass
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out.close()
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if __name__ == "__main__": __main__()
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