Slightly improved interface to merging utility for multiple bam files

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@757 348d0f76-0448-11de-a6fe-93d51630548a

python/MergeBAMBatch.py

@@ -13,7 +13,7 @@ bam_ext = '.bam'
 if __name__ == "__main__":
     usage = "usage: %prog [options]"
     parser = OptionParser(usage=usage)
-    parser.add_option("-q", "--farm", dest="farm_sub",
+    parser.add_option("-q", "--farm", dest="farmQueue",
                         type="string", default=None,
                         help="Farm queue to send processing jobs to")
     parser.add_option("-d", "--dir", dest="output_dir",
@@ -47,8 +47,8 @@ if __name__ == "__main__":
             if OPTIONS.ignoreExistingFiles or not os.path.exists(output_filename):
                 cmd = 'java -Xmx4096m -jar ' + MERGE_BIN + ' AS=true SO=coordinate O=' + output_filename + ' VALIDATION_STRINGENCY=SILENT ' + ' I=' + (' I='.join(sources))
                 print cmd
-                farm_commands.cmd(cmd, OPTIONS.farm_sub, output)
+                farm_commands.cmd(cmd, OPTIONS.farmQueue, output)
 
             if OPTIONS.ignoreExistingFiles or not os.path.exists(output_index):
-                ValidateGATK.indexBAM(output_filename)
+                ValidateGATK.indexBAM(output_filename, OPTIONS.farmQueue)
 

python/ValidateGATK.py

@@ -6,9 +6,9 @@ import string
 
 defaultCommands = ['CountReads', 'Pileup']
 
-def indexBAM(reads):
+def indexBAM(reads, queue=None):
     cmd = "samtools index " + reads
-    farm_commands.cmd(cmd, None, None)    
+    farm_commands.cmd(cmd, queue, None)    
 
 def readIntervalFile(file):
     def notHeaderP(line):

python/farm_commands.py

@@ -3,15 +3,21 @@
 import os
 #justPrintCommands = False
 
-def cmd(cmd_str, farm_queue=False, output_head="", just_print_commands=False, outputFile = None):
+def cmd(cmd_str, farm_queue=False, output_head=None, just_print_commands=False, outputFile = None):
     # if farm_queue is non-False, submits to queue, other
 
     if farm_queue:
         if outputFile <> None:
             farm_stdout = outputFile
-        else:
+        elif output_head <> None:
             farm_stdout = output_head+".stdout"
-        cmd_str = "bsub -q "+farm_queue+" -o "+farm_stdout+" "+cmd_str #+" TMP_DIR=/wga/scr1/andrewk/tmp"
+        else:
+            farm_stdout = None
+            
+        cmd_str = "bsub -q "+farm_queue+" "+cmd_str 
+        if farm_stdout <> None:
+            cmd_str += " -o " + farm_stdout
+        
         print ">>> Farming via "+cmd_str
     else:
         print ">>> Executing "+cmd_str