diff shear_wrapper.py @ 6:0158f7356ffd

Add new outputs and params to shear_sv.xml for version 2.3

--- a/shear_wrapper.py	Thu Oct 17 08:01:38 2013 -0500
+++ b/shear_wrapper.py	Mon Oct 21 08:54:58 2013 -0500
@@ -18,10 +18,12 @@
     parser.add_option( '-F', '--fasta_index', dest='fai', help='The .fai index file for the reference sequence fasta' )
     parser.add_option( '-t', '--twobit', dest='twobit', help='The .2bit encoding of the reference sequence fasta generated by faToTwoBit' )
     parser.add_option( '-i', '--bwa_index', dest='bwa_index', help='The bwa index of the reference sequence' )
-    parser.add_option( '-r', '--report', dest='report', help='The SHEAR output report' )
+    parser.add_option( '-R', '--report', dest='report', help='The SHEAR output report' )
     parser.add_option( '-s', '--sdi', dest='sdi', help='The SHEAR sdi input from the SHEAR sv command' )
     parser.add_option( '-o', '--output', dest='output', help='The SHEAR output assembly fasta file' )
     parser.add_option( '-D', '--svidx_dir', dest='svidx_dir', help='The SHEAR output assembly fasta file' )
+    parser.add_option( '-S', '--sv-only', dest='sv_only', action="store_true", help='SV Only prediction mode.' )
+    parser.add_option( '-r', '--region', dest='region', help='Region of the input alignment to analyze' )
     (options, args) = parser.parse_args()
 
     def make_ref(src, dest, copy=False):
@@ -50,6 +52,11 @@
     if command in ['sv']:
         args.append( '-p' )
         args.append( prefix )
+        if options.sv_only:
+            args.append('--sv-only')
+        if options.region:
+            args.append('-r')
+            args.append(options.region)
     if options.svidx_dir and command in ['sv']:
         if not os.path.isdir(options.svidx_dir):
             os.makedirs(options.svidx_dir)
@@ -220,19 +227,6 @@
         returncode = proc.wait()
         if returncode != 0:
             stop_err( 'Error running SHEAR ' + command, returncode )
-        if command in ['sv']:
-            report_path = os.path.join(os.getcwd(),prefix + '.report')
-            if os.path.exists(report_path):
-                if options.report:
-                    shutil.copy(report_path,options.report)
-            else:
-                raise Exception, 'no report file'
-            sdi_path = os.path.join(os.getcwd(),prefix + '.sdi')
-            if os.path.exists(sdi_path):
-                if options.sdi:
-                    shutil.copy(sdi_path,options.sdi)
-            else:
-                raise Exception, 'no sdi file'
     except Exception, e:
         # clean up temp dirs
         stop_err( 'Error running SHEAR %s %s' % (command,str(e)),9 )