Mercurial > repos > konradpaszkiewicz > velvetoptimiser
view velvet_optimiser.py @ 0:50ae1360fbbe 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 18:07:56 -0400 |
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#!/usr/bin/env python """ VelvetOptimiser Wrapper Adapted from velveth and velvetg tools in Galaxy Konrad Paszkiewicz University of Exeter, UK. """ import pkg_resources; import logging, os, string, sys, tempfile, glob, shutil, types, urllib import shlex, subprocess from optparse import OptionParser, OptionGroup from stat import * log = logging.getLogger( __name__ ) assert sys.version_info[:2] >= ( 2, 4 ) def stop_err( msg ): sys.stderr.write( "%s\n" % msg ) sys.exit() def __main__(): #Parse Command Line s = 'velvetg_optimiser.py: argv = %s\n' % (sys.argv) #print >> sys.stderr, s # so will appear as blurb for file argcnt = len(sys.argv) starthash = sys.argv[1] endhash = sys.argv[2] inputs = sys.argv[3] threads = sys.argv[4] afgFile = sys.argv[5] kmeropt = sys.argv[6] covopt = sys.argv[7] contigs = sys.argv[8] LastGraph = sys.argv[9] velvet_asm = sys.argv[10] unusedReadsFile = sys.argv[11] stats = sys.argv[12] othervelvetgoptions = sys.argv[13] working_dir = '' cmdline = '/usr/local/velvet/contrib/VelvetOptimiser-2.1.7/VelvetOptimiser.pl -s %s -e %s -f \' %s \' -t %s -a 1 -k %s -c %s -o \'-unused_reads yes %s\' 2&1>/dev/null' % (starthash, endhash, inputs, threads, kmeropt, covopt, othervelvetgoptions) #print >> sys.stderr, cmdline # so will appear as blurb for file try: proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE ) returncode = proc.wait() # get stderr, allowing for case where it's very large stderr = '' buffsize = 1048576 try: while True: stderr += proc.stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass if returncode != 0: raise Exception, stderr except Exception, e: stop_err( 'Error running velvet_optimiser.py' + str( e ) ) out = open(contigs,'w') contigs_path = os.path.join(working_dir,'contigs.fa') #print >> sys.stderr, contigs_path for line in open(contigs_path ): out.write( "%s" % (line) ) out.close() out = open(stats,'w') stats_path = os.path.join(working_dir,'stats.txt') for line in open( stats_path ): out.write( "%s" % (line) ) out.close() if LastGraph != 'None': out = open(LastGraph,'w') LastGraph_path = os.path.join(working_dir,'LastGraph') for line in open( LastGraph_path ): out.write( "%s" % (line) ) out.close() if afgFile != 'None': out = open(afgFile,'w') afgFile_path = os.path.join(working_dir,'velvet_asm.afg') try: for line in open( afgFile_path ): out.write( "%s" % (line) ) except: logging.warn( 'error reading %s' %(afgFile_path)) pass out.close() if unusedReadsFile != 'None': out = open(unusedReadsFile,'w') unusedReadsFile_path = os.path.join(working_dir,'UnusedReads.fa') try: for line in open( unusedReadsFile_path ): out.write( "%s" % (line) ) except: logging.info( 'error reading %s' %(unusedReadsFile_path)) pass out.close() if __name__ == "__main__": __main__()