From 3b1f84e15b8a63a79b5cc6563774cc3fc663aaa9 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 20 May 2009 12:54:41 +0000
Subject: [PATCH] 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 |  6 +++---
 python/ValidateGATK.py  |  4 ++--
 python/farm_commands.py | 12 +++++++++---
 3 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/python/MergeBAMBatch.py b/python/MergeBAMBatch.py
index 1facedfb4..5c643fe38 100755
--- a/python/MergeBAMBatch.py
+++ b/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)
 
diff --git a/python/ValidateGATK.py b/python/ValidateGATK.py
index 114fa6f85..9dcf77c7a 100755
--- a/python/ValidateGATK.py
+++ b/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):
diff --git a/python/farm_commands.py b/python/farm_commands.py
index f6b618c98..7d33aaf46 100644
--- a/python/farm_commands.py
+++ b/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