104 lines
4.0 KiB
Python
Executable File
104 lines
4.0 KiB
Python
Executable File
#
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# GATK configuration parser
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#
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import ConfigParser
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import os.path
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import sys
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defaultRequiredOptions = {}
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def addRequiredOption(name, type):
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defaultRequiredOptions[name] = type
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addRequiredOption('jar', 'input_file')
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addRequiredOption('reference', 'input_file')
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addRequiredOption('referenceIndex', 'input_file')
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addRequiredOption('referenceDict', 'input_file')
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addRequiredOption('java', 'file')
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addRequiredOption('jvm_args', str)
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addRequiredOption('args', str)
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addRequiredOption('tmp', 'output_file')
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class gatkConfigParser(ConfigParser.SafeConfigParser):
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GATK = 'DEFAULT'
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def __init__(self, configFiles):
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ConfigParser.SafeConfigParser.__init__(self)
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files = filter(None, configFiles)
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print 'Reading configuration file(s):', files
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self.read(files)
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self.validateRequiredOptions()
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self.moreArgs = ""
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def validateRequiredOptions(self):
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for key, value in defaultRequiredOptions.iteritems():
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self.validateOption(self.GATK, key, value)
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def validateOption(self, section, name, type = str):
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v = self.getOption(section, name, type)
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#print ' => Validated option', name, v
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def getGATKOption(self, name, type = str):
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return self.getOption(self.GATK, name, type)
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def getGATKModeOption(self, name, mode, type = str):
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return self.getOption(mode, name, type)
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def getOption(self, section, name, typeF = None):
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if not self.has_option(section, name):
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raise "Option %s not found in section %s" % (name, section)
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else:
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val = self.get(section, name)
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if typeF == 'input_file' or typeF == 'output_file':
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path = os.path.abspath(os.path.expanduser(val))
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if typeF == 'input_file':
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if not os.path.exists(path):
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raise "Input file does not exist", path
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if not os.access(path, os.R_OK):
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raise "Input file cannot be read", path
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if typeF == 'output_file':
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if not os.access(path, os.W_OK):
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raise "Output file cannot be written", path
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return path
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elif type(typeF) == str:
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return str(val)
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elif typeF == None:
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return val
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else:
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return typeF(val)
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def java(self): return self.getOption(self.GATK, 'java')
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def jvm_args(self): return self.getOption(self.GATK, 'jvm_args')
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def jar(self): return self.getOption(self.GATK, 'jar')
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def gatk_args(self): return self.getOption(self.GATK, 'args')
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def reference(self): return self.getOption(self.GATK, 'reference')
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def setMoreArgs(self, s):
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self.moreArgs = s
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def gatkCmd(self, mode, log = None, stdLogName=False):
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cmd = ' '.join([self.java(), self.jvm_args(), '-jar', self.jar(), self.gatk_args(), '-R', self.reference()])
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cmd += ' ' + ' '.join(['-T', mode, self.getGATKModeOption('args', mode)]) + ' ' + self.moreArgs
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if log <> None:
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if stdLogName:
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#head, ext = os.path.splitext(log)
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logName = log + "." + mode + ".log"
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else:
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logName = log
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cmd += ' ' + ' '.join(['-log', logName])
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return cmd
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import unittest
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class TestMergeBAMsUtils(unittest.TestCase):
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def setUp(self):
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configFile = os.path.join(os.path.split(sys.argv[0])[0] + "/../testdata/defaultGATKConfig.cfg")
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self.config = gatkConfigParser(configFile)
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def testValidate(self):
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self.config.validateRequiredOptions()
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#def testCmd(self):
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# s = "java -ea -Xmx2048m -jar ~/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar -l INFO -L 1:1-10,000,000 -R /home/radon01/depristo/work/humanref/Homo_sapiens_assembly18.fasta -T CountCovariates --MIN_MAPPING_QUALITY 1"
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# self.assertEquals(self.config.gatkCmd('CountCovariates'), s)
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if __name__ == '__main__':
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unittest.main() |