diff oases_optimiser.py @ 4:dc684e37f668 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_oases commit 47a8a06faad1aa3c36503934ee2fd9e6031d3b75

--- a/oases_optimiser.py	Tue Sep 29 06:29:42 2015 -0400
+++ b/oases_optimiser.py	Thu May 12 10:45:03 2016 -0400
@@ -6,50 +6,48 @@
 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 *
+import os, sys
+import subprocess
 
 
-def stop_err( msg ):
-    sys.stderr.write( "%s\n" % msg )
+def stop_err(msg):
+    sys.stderr.write("%s\n" % msg)
     sys.exit()
 
-def oases_optimiser(starthash, endhash, input, job_dir):
+
+def oases_optimiser(starthash, endhash, input):
     '''
     Replaces call to oases_optimiser.sh. For all k-mers between
     starthash and endhash run velvet and oases.
     '''
     for i in xrange(starthash, endhash, 2):
-        cmd1="velveth {0}/outputFolder_{1} {1} {2} && ".format(job_dir, i, input)
-        cmd2="velvetg {0}/outputFolder_{1} -read_trkg yes && ".format(job_dir, i)
-        cmd3="oases {0}/outputFolder_{1}".format(job_dir, i)
-        proc = subprocess.call( args=cmd1+cmd2+cmd3, shell=True, stdout=sys.stdout, stderr=sys.stderr )
-    cmd4="velveth {0}/MergedAssemblyFolder 27 -long outputFolder_*/transcripts.fa && ".format(job_dir)
-    cmd5="velvetg {0}/MergedAssemblyFolder -read_trkg yes -conserveLong yes && ".format(job_dir)
-    cmd6="oases {0}/MergedAssemblyFolder -merge yes".format(job_dir)
-    proc = subprocess.call( args=cmd4+cmd5+cmd6, shell=True, stdout=sys.stdout, stderr=sys.stderr )
+        cmd1 = "velveth outputFolder_{0} {0} {1} && ".format(i, input)
+        cmd2 = "velvetg outputFolder_{0} -read_trkg yes && ".format(i)
+        cmd3 = "oases outputFolder_{0}".format(i)
+        proc = subprocess.call(args=cmd1 + cmd2 + cmd3, shell=True, stdout=sys.stdout, stderr=sys.stdout)
+        if not proc == 0:
+            print("Oases failed at k-mer %s, skipping" % i)
+            continue
+    cmd4 = "velveth MergedAssemblyFolder 27 -long outputFolder_*/transcripts.fa && "
+    cmd5 = "velvetg MergedAssemblyFolder -read_trkg yes -conserveLong yes && "
+    cmd6 = "oases MergedAssemblyFolder -merge yes"
+    proc = subprocess.call(args=cmd4 + cmd5 + cmd6, shell=True, stdout=sys.stdout, stderr=sys.stdout)
+    if not proc == 0:
+        raise Exception("Oases could not merge assembly")
 
 def __main__():
-    job_dir= os.getcwd()
-    #Parse Command Line
     starthash = int(sys.argv[1])
     endhash = int(sys.argv[2])
     input = sys.argv[3]
     transcripts = sys.argv[4]
-    transcripts_path = ''
-    print >> sys.stdout, "PATH = %s" % (os.environ['PATH'])
     try:
-        oases_optimiser(starthash, endhash, input, job_dir)
+        oases_optimiser(starthash, endhash, input)
     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()
- 
+        stop_err('Error running oases_optimiser.py\n' + str(e))
+    with open(transcripts, 'w') as out:
+        transcript_path = os.path.join("MergedAssemblyFolder", 'transcripts.fa')
+        for line in open(transcript_path):
+            out.write("%s" % (line))
+
+
 if __name__ == "__main__": __main__()