--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/edge_pro.py	Mon Sep 09 06:11:47 2013 -0400
@@ -0,0 +1,107 @@
+# -*- coding: utf-8 -*-
+"""
+Wrapper for EDGE - Gene expression in Prokaryotes
+Author: Paolo Uva paolo dot uva at crs4 dot it
+Date: March 18, 2013
+"""
+
+import glob
+import optparse
+import os
+import shutil
+import subprocess
+import tempfile
+import sys
+
+def __main__():
+    # Parse Command Line
+    parser = optparse.OptionParser()
+    # Input
+    parser.add_option('-g', '--genome', dest="genome")
+    parser.add_option('-p', '--ptt', dest="ptt")
+    parser.add_option('-r', '--rnt', dest="rnt")
+    parser.add_option('-u', '--input1', dest="input1")
+    parser.add_option('-v', '--input2', dest="input2")
+    parser.add_option('-t', '--num-threads', dest="num_threads", type='int')
+    parser.add_option('-m', '--minInsertSize', dest="minInsertSize", type='int')
+    parser.add_option('-M', '--maxInsertSize', dest="maxInsertSize", type='int')
+    parser.add_option('-w', '--window', dest="window", type='int')
+    parser.add_option('-i', '--utrSize', dest="utrSize", type='int')
+    parser.add_option('-x', '--similarity', dest="similarity", type='float')
+    parser.add_option('-c', '--minCoverage', dest="minCoverage", type='int')
+    parser.add_option('-l', '--readLength', dest="readLength", type='int')
+    # Output
+    parser.add_option('--out-aln', dest="out_aln")
+    parser.add_option('--out-rpkm', dest="out_rpkm")
+    parser.add_option('--out-log', dest="out_log")
+    (options, args) = parser.parse_args()
+    if len(args) > 0:
+        parser.error('Wrong number of arguments')
+    
+    # Build command
+    if options.input2:
+        input2_flag = '-v %s' % (options.input2)
+    else:
+        input2_flag = ''
+    if options.num_threads is not None:
+        num_threads_flag = '-t %d' % options.num_threads
+    else:
+        num_threads_flag = ''
+    if options.minInsertSize is not None:
+        minInsertSize_flag = '-m %d' % options.minInsertSize
+    else:
+        minInsertSize_flag = ''
+    if options.maxInsertSize is not None:
+        maxInsertSize_flag = '-M %d' % options.maxInsertSize
+    else:
+        maxInsertSize_flag = ''
+    if options.window is not None:
+        window_flag = '-w %d' % options.window
+    else:
+        window_flag = ''
+    if options.utrSize is not None:
+        utrSize_flag = '-i %d' % options.utrSize
+    else:
+        utrSize_flag = ''
+    if options.similarity is not None:
+        similarity_flag = '-x %s' % options.similarity
+    else:
+        similarity_flag = ''
+    if options.readLength is not None:
+        readLength_flag = '-l %d' % (options.readLength)
+    else:
+        readLength_flag = ''
+    if options.minCoverage is not None:
+        minCoverage_flag = '-c %d' % options.minCoverage
+    else:
+        minCoverage_flag = ''
+    
+    wd = tempfile.mkdtemp()
+    try:
+        prefix = os.path.join(wd, 'out')
+        cl = 'edge.pl -g %s -p %s -r %s -u %s -o %s %s %s %s %s %s %s %s %s %s' % (options.genome, options.ptt, options.rnt, options.input1, prefix, input2_flag, num_threads_flag, minInsertSize_flag, maxInsertSize_flag, window_flag, utrSize_flag, similarity_flag, readLength_flag, minCoverage_flag)
+        print cl
+        
+        if options.out_log:
+            sout = open(options.out_log, 'w')
+        else:
+            sout = sys.stdout
+        try:
+            subprocess.check_call(cl, stdout=sout, stderr=subprocess.STDOUT, shell=True) # need to redirect stderr because edge.pl calls bowtie2 and count which write some logging info there
+        finally:
+            if sout != sys.stdout:
+                sout.close()
+
+        # Move alignment file
+        shutil.move(prefix + '.alignments', options.out_aln)
+        # Concatenate multiple RPKM files together
+        with open(options.out_rpkm, 'wb') as destination:
+            for filename in glob.iglob(prefix + '.rpkm_*'):
+                with open(filename, 'rb') as source:
+                    shutil.copyfileobj(source, destination)
+    finally:
+        shutil.rmtree(wd)
+
+
+if __name__ == "__main__":
+    __main__()