diff velvet_optimiser.py @ 0:50ae1360fbbe default tip

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

--- /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__()