39 lines
1.1 KiB
Python
Executable File
39 lines
1.1 KiB
Python
Executable File
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)
|
|
|
|
|