Mercurial > repos > konradpaszkiewicz > velvetoptimiser
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/velvet_optimiser.py Tue Jun 07 18:07:56 2011 -0400 @@ -0,0 +1,102 @@ +#!/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__()