Stress Test utility for pushing the GATK to its limits. Takes a list of sam files and runs Analyses on them all, optionally in the queue

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@98 348d0f76-0448-11de-a6fe-93d51630548a

playground/python/StressTestGATK.py

@@ -0,0 +1,38 @@
+import farm_commands
+import os.path
+import sys
+import getopt
+
+def usage():
+    print "Optional arguments:"
+    print "  -f QUEUE   Farm jobs to QUEUE on LSF"
+
+if __name__ == "__main__":
+    opts = None
+    try:
+        opts, args = getopt.getopt(sys.argv[1:], "f:", ["farm"])
+    except getopt.GetoptError:
+        print sys.argv
+        usage()
+        sys.exit(2)
+
+    farm_sub = False
+
+    for opt, arg in opts:
+        if opt in ("-f", "--farm"):
+            farm_sub = arg
+
+    for line in open(sys.argv[1]):
+        lane = line.strip()
+        head, lane_filename = os.path.split(lane)
+        filebase = os.path.splitext(lane_filename)[0]
+    
+        # convert the fasta
+        for analysis in ['CountLoci', 'Pileup']:
+            output = filebase + '.' + analysis + '.output'
+            if not os.path.exists(output):
+                cmd = "java -jar ~/dev/GenomeAnalysisTK/trunk/playground/java/dist/GenomeAnalysisTK.jar T=" + analysis + " I= " + lane + " R= /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"
+                print cmd
+                farm_commands.cmd(cmd, farm_sub, output, just_print_commands=True)
+
+