129 lines
4.8 KiB
Python
Executable File
129 lines
4.8 KiB
Python
Executable File
from farm_commands2 import *
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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 datetime import date
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import glob
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import operator
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import faiReader
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import math
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import shutil
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import string
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GATK_STABLE_JAR = '/home/radon01/depristo/dev/GenomeAnalysisTKStable/trunk/dist/GenomeAnalysisTK.jar'
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GATK_DEV_JAR = '/home/radon01/depristo/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar'
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GATK_JAR = GATK_STABLE_JAR
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# add to GATK to enable dbSNP aware cleaning
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# -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod
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hg18 = ['chrM'] + ['chr' + str(i) for i in range(1,23)] + ['chrX', 'chrY']
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b36 = [str(i) for i in range(1,23)] + ['X', 'Y', 'MT']
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#hg18 = ['chr' + str(i) for i in range(1,23)] + ['chrX', 'chrY']
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#b36 = [str(i) for i in range(1,23)] + ['X', 'Y']
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HG18_TO_B36 = {
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'hg18' : 'b36',
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'/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta' : '/broad/1KG/reference/human_b36_both.fasta',
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'/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta.fai' : '/broad/1KG/reference/human_b36_both.fasta.fai',
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'chrM' : 'MT',
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'chr' : '' }
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def hg18args_to_b36(s):
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for key, value in HG18_TO_B36.iteritems():
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s = s.replace(key, value)
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return s
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def appendExtension(path, newExt, addExtension = True):
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root, basename = os.path.split(path)
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basename, ext = os.path.splitext(basename)
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print root, basename, ext, path
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s = basename + '.' + newExt
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if addExtension: s += ext
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return os.path.join(root, s)
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# return os.path.join(OPTIONS.dir, s)
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class PipelineArgs:
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def __init__( self, GATK_JAR = GATK_JAR, ref = 'hg18', name = None, memory = '3g', excludeChrs = [] ):
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self.GATK = 'java -Xmx%s -Djava.io.tmpdir=/broad/shptmp/depristo/tmp/ -jar ' + GATK_JAR + ' -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -l INFO '
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self.ref = ref
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self.name = name
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self.memory = memory
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self.excludeChrs = excludeChrs
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def convertToB36(self):
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return self.ref == 'b36'
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def addGATKArg(self, arg):
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if len(arg) > 0 and arg[0] != ' ':
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arg = ' ' + arg
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self.GATK += arg
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def getCommandName(self, suffix):
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if self.name != None:
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return self.name + "." + suffix
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else:
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return suffix
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def finalizedGATKCommand(self, args):
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cmd = (self.GATK % self.memory) + ' ' + args
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if self.convertToB36():
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cmd = hg18args_to_b36(cmd)
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return cmd
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def chrsToSplitBy(self, chrs):
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return filter(lambda x: x not in self.excludeChrs, chrs)
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#
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# General features
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#
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def simpleGATKCommand( pargs, name, args, lastJobs ):
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cmd = pargs.finalizedGATKCommand(args)
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return [FarmJob(cmd, jobName = pargs.getCommandName(name), dependencies = lastJobs)]
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#
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# Takes a simpleGATKCommand and splits it by chromosome, merging output
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#
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def splitGATKCommandByChr( myPipelineArgs, cmd, outputsToParallelize, mergeCommands ):
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if cmd.cmd_str_from_user.find(" -L") != -1:
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sys.exit("Found -L argument in command -- cannot be provided for parallelization by chromosome: " + cmd.cmd_str_from_user)
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def makeChrCmd(chr):
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chrOutputMap = map(lambda x: appendExtension(x, chr), outputsToParallelize)
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chr_cmd_str = cmd.cmd_str_from_user
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chr_cmd_str += ' -L ' + chr
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for x, y in zip(outputsToParallelize, chrOutputMap):
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chr_cmd_str = chr_cmd_str.replace(x, y)
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if myPipelineArgs.convertToB36():
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chr_cmd_str = hg18args_to_b36(chr_cmd_str)
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chrCmd = FarmJob(chr_cmd_str, jobName = cmd.jobName + '.byChr' + chr, dependencies = cmd.dependencies)
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return chrCmd, chrOutputMap
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splits = map( makeChrCmd, myPipelineArgs.chrsToSplitBy(hg18) )
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splitCommands = map(lambda x: x[0], splits)
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def mergeCommand1(i):
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mergeCommand = mergeCommands[i]
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mergeFile = outputsToParallelize[i]
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splitFiles = map(lambda x: x[1][i], splits)
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return FarmJob(mergeCommand(splitFiles, mergeFile), jobName = cmd.jobName + '.merge', dependencies = splitCommands)
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mergeCommands = map(mergeCommand1, range(len(outputsToParallelize)))
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return splitCommands + mergeCommands
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def mergeVCFs(splitFiles, mergeFile):
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splitFilesString = ' '.join(splitFiles)
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cmd = "python ~/dev/GenomeAnalysisTK/trunk/python/mergeVCFs.py -a -f /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta.fai %s > %s" % (splitFilesString, mergeFile)
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return cmd
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def mergeByCat(splitFiles, mergeFile):
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splitFilesString = ' '.join(splitFiles)
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return "cat %s > %s" % (splitFilesString, mergeFile)
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def indexBAMFile( name, bamFile, lastJobs ):
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cmd = 'samtools index ' + bamFile
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return [FarmJob(cmd, jobName = 'samtools.index.' + name, dependencies = lastJobs)], None
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