--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/panama_run.py	Sun Jun 16 12:24:55 2013 +0530
@@ -0,0 +1,71 @@
+#!/usr/bin/env python
+"""
+Run panama on expression and snp data
+usage: panama_run.py [options]
+   --exp_data: Expression data CSV file
+   --snp_data: SNP data file
+   --output1: Output CSV dataset
+"""
+
+import optparse, os, sys, subprocess, tempfile, shutil
+from galaxy import eggs
+import pkg_resources; pkg_resources.require( "bx-python" )
+from bx.cookbook import doc_optparse
+from galaxy import util
+
+def stop_err( msg ):
+    sys.stderr.write( '%s\n' % msg )
+    sys.exit()
+
+
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '', '--exp_data', dest='exp_data', help='The input Expression dataset')
+    parser.add_option( '', '--snp_data', dest='snp_data', help='The input snp dataset' )
+    parser.add_option( '', '--output1', dest='output1', help='The output CSV dataset' )
+    ( options, args ) = parser.parse_args()
+
+    try:
+        tmp_dir = tempfile.mkdtemp()
+        panama_output_file_name = os.path.join(tmp_dir, "PANAMA_results.csv")
+        command = 'panama %s %s -d %s' %(options.exp_data,options.snp_data,tmp_dir)
+        print command
+        tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
+        tmp_stderr = open( tmp, 'wb' )
+        proc = subprocess.Popen( args=command, shell=True, stderr=tmp_stderr.fileno() )
+        returncode = proc.wait()
+        tmp_stderr.close()
+        # get stderr, allowing for case where it's very large
+        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()
+        if returncode != 0:
+            raise Exception, stderr
+    except Exception, e:
+        #clean up temp files
+        print e
+        if os.path.exists( tmp_dir ):
+            shutil.rmtree( tmp_dir )
+        stop_err( 'Error opening panama')
+    # Move tmp_aligns_file_name to our output dataset location
+    shutil.move( panama_output_file_name, options.output1 )
+    #clean up temp files
+    if os.path.exists( tmp_dir ):
+        shutil.rmtree( tmp_dir )
+    # check that there are results in the output file
+    if os.path.getsize( options.output1 ) > 0:
+        sys.stdout.write( 'PANAM results generated' )
+    else:
+        stop_err( 'Error generating PANAMA results' )
+
+if __name__=="__main__": __main__()