81 lines
3.7 KiB
Python
Executable File
81 lines
3.7 KiB
Python
Executable File
import farm_commands
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import os.path
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import sys
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from optparse import OptionParser
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from gatkConfigParser import *
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import glob
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if __name__ == "__main__":
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usage = """usage: %prog [-c config.cfg]* input.bam output.bam"""
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parser = OptionParser(usage=usage)
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parser.add_option("-A", "--args", dest="args",
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type="string", default="",
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help="arguments to GATK")
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parser.add_option("-C", "--CovariateArgs", dest="CovariateArgs",
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type="string", default="",
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help="arguments to GATK")
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parser.add_option("-q", "--farm", dest="farmQueue",
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type="string", default=None,
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help="Farm queue to send processing jobs to")
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parser.add_option("-c", "--config", dest="configs",
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action="append", type="string", default=[],
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help="Configuration file")
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parser.add_option("-d", "--dir", dest="scratchDir",
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type="string", default="test",
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help="Output directory")
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parser.add_option("", "--dry", dest="dry",
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action='store_true', default=False,
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help="If provided, nothing actually gets run, just a dry run")
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parser.add_option("", "--plot", dest="plot",
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action='store_true', default=False,
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help="If provided, will call R to generate convenient plots about the Q scores of the pre and post calibrated files")
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parser.add_option("-i", "--ignoreExistingFiles", dest="ignoreExistingFiles",
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action='store_true', default=False,
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help="Ignores already written files, if present")
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(OPTIONS, args) = parser.parse_args()
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if len(args) != 2:
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parser.error("incorrect number of arguments")
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config = gatkConfigParser(OPTIONS.configs)
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inputBAM = args[0]
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outputBAM = args[1]
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rootname = os.path.split(os.path.splitext(outputBAM)[0])[1]
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covariateRoot = os.path.join(OPTIONS.scratchDir, rootname)
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covariateInitial = covariateRoot + '.init'
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initDataFile = covariateInitial + '.raw_data.csv'
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covariateRecal = covariateRoot + '.recal'
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recalDataFile = covariateRecal + '.raw_data.csv'
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if not os.path.exists(OPTIONS.scratchDir):
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os.mkdir(OPTIONS.scratchDir)
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def covariateCmd(bam, outputDir, ignoreAdds):
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add = " -I %s --OUTPUT_FILEROOT %s" % (bam, outputDir)
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if not ignoreAdds:
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add += " " + OPTIONS.CovariateArgs
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return config.gatkCmd('CountCovariates') + add
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def recalibrateCmd(inputBAM, dataFile, outputBAM):
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return config.gatkCmd('TableRecalibration') + " -I %s -params %s -outputBAM %s" % (inputBAM, dataFile, outputBAM)
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def runCovariateCmd(inputBAM, dataFile, dir, jobid, ignoreAdds = False):
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if OPTIONS.ignoreExistingFiles or not os.path.exists(dataFile):
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cmd = covariateCmd(inputBAM, dir, ignoreAdds)
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return farm_commands.cmd(cmd, OPTIONS.farmQueue, None, just_print_commands = OPTIONS.dry, waitID = jobid)
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#
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# Actually do some work here
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#
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jobid = None
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jobid = runCovariateCmd(inputBAM, initDataFile, covariateInitial, jobid, False)
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if OPTIONS.ignoreExistingFiles or not os.path.exists(outputBAM):
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cmd = recalibrateCmd(inputBAM, initDataFile, outputBAM)
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, None, just_print_commands = OPTIONS.dry, waitID = jobid)
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jobid = farm_commands.cmd('samtools index ' + outputBAM, OPTIONS.farmQueue, None, just_print_commands = OPTIONS.dry, waitID = jobid)
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jobid = runCovariateCmd(outputBAM, recalDataFile, covariateRecal, jobid, True)
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