diff oases_optimiser.py @ 0:eedbe32980bb draft

planemo upload for repository https://bitbucket.org/drosofff/gedtools/

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/oases_optimiser.py	Sun Jun 21 14:38:06 2015 -0400
@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+
+"""
+VelvetOptimiser Wrapper
+refactored using the adaptation of
+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 *
+
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+
+def __main__():
+    job_dir= os.getcwd()
+    #tmp_work_dir = tempfile.mkdtemp(dir = job_dir) # make temp directory in the job_dir
+    #Parse Command Line
+    starthash = sys.argv[1]
+    endhash = sys.argv[2]
+    inputs = sys.argv[3]
+    transcripts = sys.argv[4]
+    transcripts_path = ''
+    cmdline = "oases_optimiser.sh %s %s '%s' %s  2&1>/dev/null" % (starthash, endhash, inputs, job_dir) # 2&1>/dev/null
+    print >> sys.stdout, cmdline # so will appear as blurb for file
+    print >> sys.stdout, job_dir
+    print >> sys.stdout, "PATH = %s" % (os.environ['PATH'])
+    try:
+        proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE ) #  cwd=job_dir
+        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 oases_optimiser.py' + str( e ) )
+    out = open(transcripts,'w')
+    transcript_path = os.path.join(job_dir, "MergedAssemblyFolder", 'transcripts.fa')
+    print >> sys.stdout, transcript_path
+    for line in open(transcript_path):
+        out.write( "%s" % (line) )
+    out.close()
+ 
+if __name__ == "__main__": __main__()