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Better stress test 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@113 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-03-20 15:52:54 +00:00
parent 3565b50ff5
commit 322f4b944f
1 changed files with 8 additions and 5 deletions
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9
playground/python/StressTestGATK.py
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@ -13,7 +13,7 @@ def usage():
if __name__ == "__main__": if __name__ == "__main__":
opts = None opts = None
try: try:
opts, args = getopt.getopt(sys.argv[1:], "f:c:", ["farm", "commands"]) opts, args = getopt.getopt(sys.argv[1:], "f:c:i", ["farm", "commands", "ignoreExistingFiles"])
except getopt.GetoptError: except getopt.GetoptError:
print sys.argv print sys.argv
usage() usage()
@ -21,12 +21,15 @@ if __name__ == "__main__":
farm_sub = False farm_sub = False
commandsList = defaultCommands commandsList = defaultCommands
ignoreExistingFiles = False
for opt, arg in opts: for opt, arg in opts:
if opt in ("-f", "--farm"): if opt in ("-f", "--farm"):
farm_sub = arg farm_sub = arg
if opt in ("-c", "--commands"): if opt in ("-c", "--commands"):
commandsList = arg.split(',') commandsList = arg.split(',')
if opt in ("-e", "--ignoreExistingFiles"):
ignoreExistingFiles = True
for line in open(args[0]): for line in open(args[0]):
lane = line.strip() lane = line.strip()
@ -36,8 +39,8 @@ if __name__ == "__main__":
# convert the fasta # convert the fasta
for analysis in commandsList: for analysis in commandsList:
output = filebase + '.' + analysis + '.output' output = filebase + '.' + analysis + '.output'
#if not os.path.exists(output): if ignoreExistingFiles or 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 " cmd = "java -jar ~/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar T=" + analysis + " I= " + lane + " R= /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta "
print cmd print cmd
farm_commands.cmd(cmd, farm_sub, output) farm_commands.cmd(cmd, farm_sub, output)