--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/stampy_wrapper.py	Wed Dec 17 10:16:35 2014 -0500
@@ -0,0 +1,115 @@
+#!/usr/bin/env python
+
+import optparse, os, shutil, subprocess, sys, tempfile, fileinput, commands
+import time
+import re
+import psutil
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+  
+def __main__():
+    #Parse Command Line
+    start = time.time()
+    #print "start time", start
+    parser = optparse.OptionParser()
+    parser.add_option( '-s','--species',dest='species')
+    parser.add_option( '-a', '--assembly', dest='assembly' )
+    parser.add_option( '-G', '--genome_index', dest='genome_index' )
+    parser.add_option( '-e', '--genome', dest='genome')
+    parser.add_option( '-D', '--indexes-path', dest='index_path', help='Indexes directory; location of .stidx and .sthash files.' )
+
+    # Wrapper options.
+    parser.add_option( '-O', '--output', dest='output' )
+    parser.add_option( '-1', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' )
+    parser.add_option( '-2', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' )
+    parser.add_option( '-g', '--use_genome', dest='use_genome' )
+    parser.add_option( '-H', '--hashbuild', dest='build_hash' )
+    parser.add_option( '-M', '--map', dest='map', action="store_true" )
+
+    # Read group options.
+    parser.add_option( '-d', '--sd', dest='sd' )
+    parser.add_option( '-i', '--insert', dest='insert' )
+    parser.add_option( '-r', '--subrate', dest='subrate' )
+    
+    parser.add_option( '-t', '--settings', dest='settings' )
+
+ 
+    (options, args) = parser.parse_args()
+    
+    # Creat genome index if necessary.
+    tmp_index_dir = tempfile.mkdtemp()
+    
+    # Genome index from history
+    if options.genome_index:
+        index_path = os.path.join( tmp_index_dir, '.'.join( os.path.split( options.genome_index )[1].split( '.' )[:-1] ) )
+        try:
+            os.link( options.genome_index, index_path + '.fa' )
+            #print  options.genome_index
+        except:
+            pass
+        # Indexing genome
+        cmd_index = 'stampy.py --species=%s --assembly=%s -G %s %s' %(options.species,options.assembly,options.genome_index,options.genome)
+        #print cmd_index
+        #print options.genome
+
+        try:
+            tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
+            tmp_stderr = open( tmp, 'wb' )
+            proc=subprocess.Popen(cmd_index,shell=True) 
+            returncode = proc.wait()
+            tmp_stderr.close()
+            tmp_stderr = open( tmp, 'rb' )
+            stderr = ''
+            buffsize = 1048576
+            try:
+                while True:
+                    stderr += tmp_stderr.read( buffsize )
+                    if not stderr or len( stderr ) % buffsize != 0:
+                        break
+            except OverflowError:
+                pass
+            tmp_stderr.close()
+
+        except Exception, e:
+            if os.path.exists( tmp_index_dir ):
+                shutil.rmtree( tmp_index_dir )
+            stop_err( 'Error indexing reference sequence\n' + str( e ) )
+    else:
+        index_path = options.index_path
+    try:
+        tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir).name
+        tmp_stderr = open( tmp, 'wb' )
+        # Hashing genome
+        cmd_index2 = 'stampy.py -g %s -H %s > %s' %(options.genome_index,options.genome_index,options.output)
+        #print cmd_index2
+        proc=subprocess.Popen(cmd_index2, shell=True)
+        returncode = proc.wait()
+	#print proc.returncode
+
+    except Exception, e:
+        if os.path.exists( tmp_index_dir ):
+           shutil.rmtree( tmp_index_dir )
+    cmd_index3 = 'stampy.py -g %s -h %s' %(options.genome_index,options.genome_index)
+    if options.settings == "full":
+        opts = ' --insertsize=%s --insertsd=%s --substitutionrate=%s -M %s %s > %s' %(options.insert,options.sd,options.subrate,options.input1,options.input2,options.output) 
+    else:
+    	opts = '-M %s %s > %s' %(options.input1,options.input2,options.output) 
+    cmd_index3 += opts
+    try:
+        tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
+        tmp_stderr = open( tmp, 'wb' )
+   	#print cmd_index3
+   	proc=subprocess.call(cmd_index3, shell=True)
+    except Exception, e:
+        if os.path.exists( tmp_index_dir ):
+           shutil.rmtree( tmp_index_dir )
+
+    end =  time.time() 
+    #print "end time", end
+    elapsed = end - start  
+    #print ("Time elapsed: {0:4f}sec",format(elapsed)) 
+        
+if __name__=="__main__": __main__()
+
+