67 lines
2.3 KiB
Python
Executable File
67 lines
2.3 KiB
Python
Executable File
import farm_commands
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import os.path
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import sys
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import getopt
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defaultCommands = ['CountReads', 'Pileup']
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def usage():
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print "Optional arguments:"
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print " -f QUEUE Farm jobs to QUEUE on LSF"
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print " -c cmd1,cmd2 Walkers to execute, otherwise", ' '.join(defaultCommands)
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print " -e Ignore existing files", ' '.join(defaultCommands)
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if __name__ == "__main__":
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opts = None
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try:
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opts, args = getopt.getopt(sys.argv[1:], "f:c:a:e", ["farm", "commands", "args", "ignoreExistingFiles"])
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except getopt.GetoptError:
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print sys.argv
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usage()
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sys.exit(2)
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farm_sub = False
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commandsList = defaultCommands
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ignoreExistingFiles = False
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extraArgs = ''
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for opt, arg in opts:
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if opt in ("-f", "--farm"):
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farm_sub = arg
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if opt in ("-c", "--commands"):
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commandsList = arg.split(',')
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if opt in ("-e", "--ignoreExistingFiles"):
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ignoreExistingFiles = True
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if opt in ("-a", "--args"):
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extraArgs = arg
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directory = args[1]
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for line in open(args[0]):
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lineParts = line.split()
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lane = lineParts[0].strip()
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ref = '/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta'
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if ( len(lineParts) > 1 ):
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ref = lineParts[1].strip()
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if not os.path.exists(lane):
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print 'Input SAM/BAM file: "', lane, '" does not exist, skipping...'
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continue
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head, lane_filename = os.path.split(lane)
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filebase = os.path.splitext(lane_filename)[0]
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# make the pileup
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# 503 8:03 samtools view -b MV1994.bam Escherichia_coli_K12:10-1000 > sub.bam
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# 504 8:03 samtools pileup -f Escherichia_coli_K12_MG1655.fasta sub.bam
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# convert the fasta
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for analysis in commandsList:
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output = os.path.join(directory, filebase + '.' + analysis + '.output')
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if ignoreExistingFiles or not os.path.exists(output):
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cmd = "java -jar ~/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar -T " + analysis + " -I " + lane + " -R " + ref + " -o " + output + " -l INFO " + extraArgs
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print cmd
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farm_commands.cmd(cmd, farm_sub, output)
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