diff preppereads_fasta.py @ 0:4d237a31970b 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/preppereads_fasta.py	Tue Jun 07 17:42:21 2011 -0400
@@ -0,0 +1,64 @@
+#!/usr/bin/env python
+
+"""
+Classes encapsulating decypher tool.
+James E Johnson - University of Minnesota
+"""
+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 = 'preppereads.py:  argv = %s\n' % (sys.argv)
+    # print >> sys.stderr, s # so will appear as blurb for file
+    argcnt = len(sys.argv)
+    working_dir = sys.argv[1]
+    input1 = sys.argv[2]
+    input2 = sys.argv[3]
+    outpe = sys.argv[4]
+    outsingletons = sys.argv[5]
+    cmdline = '/users/galaxy/galaxyscripts/prepare_pe_reads_for_velvet_fasta.sh %s %s %s %s %s %s > /dev/null' % (input1, '1.fastq', input2, '2.fastq', 'single.fq', 'pe.fq')
+    #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 preppereads.sh ' + str( e ) )
+
+    out = open(outpe,'w')
+    #outpe_path = os.path.join(working_dir,'')
+    for line in open('pe.fq'):
+        out.write( "%s" % (line) )
+    out.close()
+
+    out = open(outsingletons,'w')
+    #singletons_path = os.path.join(working_dir,'')
+    for line in open('single.fq'):
+        out.write( "%s" % (line) )
+    out.close()
+
+if __name__ == "__main__": __main__()