65 lines
3.8 KiB
Python
Executable File
65 lines
3.8 KiB
Python
Executable File
#!/usr/bin/python
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import os,sys
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from farm_commands import cmd
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def get_line_number_from_file(filename, line_num):
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for index, line in enumerate(open(filename)):
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if index == line_num:
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return line
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if __name__ == "__main__":
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from optparse import OptionParser
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class OptionParser (OptionParser):
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def check_required (self, opts):
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for opt in opts:
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option = self.get_option(opt)
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# Assumes the option's 'default' is set to None!
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if getattr(self.values, option.dest) is None:
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self.error("%s option not supplied" % option)
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parser = OptionParser()
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parser.add_option("-q", "--queue", help="Queue to submit jobs to (default: long)", dest="queue", default="long")
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parser.add_option("-l", "--lane", help="Lane number to process", dest="lane", default="")
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parser.add_option("-t", "--tmpdir", help="Temp directory to use", dest="tmpdir")
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parser.add_option("-b", "--barcodes", help="File with barcodes as \"Id[TABa]barcode_sequence\" with one header line", dest="barcodes")
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parser.add_option("-a", "--baits", help="Bait interval list (default: 1KG bait list)", dest="ti", default="/seq/references/HybSelOligos/thousand_genomes_alpha_redesign/thousand_genomes_alpha_redesign.baits.interval_list")
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parser.add_option("-r", "--targets", help="Target interval list (default: 1KG target list)", dest="ti", default="/seq/references/HybSelOligos/thousand_genomes_alpha_redesign/thousand_genomes_alpha_redesign.targets.interval_list")
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(options, args) = parser.parse_args()
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parser.check_required(("-l","-t","-b"))
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solexa_dir = "."
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barcodes = []
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barcode_file = open(options.barcodes) #"../barcode_sequences.txt")
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barcode_file.readline()
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for line in barcode_file:
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fields = line.split()
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barcodes.append(fields[1])
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farm = options.queue
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lane = options.lane
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alias = "lane"+str(lane)
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tmp_dir = options.tmpdir #"/humgen/gsa-scr1/andrewk/tmp/"
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cmd("/seq/software/picard/current/bin/ExtractIlluminaBarcodes.jar B="+solexa_dir+" L="+str(lane)+" BARCODE_POSITION=1 METRICS_FILE=metrics.out BARCODE=" + " BARCODE=".join(barcodes))
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cmd( "/seq/software/picard/current/bin/BustardToSam.jar B="+solexa_dir+" L="+str(lane)+" O="+alias+".bam SAMPLE_ALIAS="+alias+" RUN_BARCODE="+alias+" TMP_DIR="+tmp_dir)#, farm_queue=farm) #PAIRED_RUN=True
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for barcode in barcodes:
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id1 = cmd( "/seq/software/picard/current/bin/BustardToSam.jar B="+solexa_dir+" L="+str(lane)+" BARCODE_POSITION=1 BARCODE="+barcode+" O="+barcode+".bam RUN_BARCODE="+barcode+" SAMPLE_ALIAS=lane5 TMP_DIR="+tmp_dir, farm_queue=farm) #PAIRED_RUN=True
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id2 = cmd( "/home/radon01/andrewk/dev/Sting/trunk/python/AlignBam.py "+barcode+".bam", farm_queue=farm, waitID = id1)
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id3 = cmd("/seq/software/picard/1.21/bin/MergeSamFiles.jar I="+barcode+".aligned.bam O="+barcode+".aligned.merged.bam VALIDATION_STRINGENCY=SILENT", farm_queue=farm, waitID = id2)
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id4 = cmd("java -Xmx4096m -jar /seq/software/picard/1.21/bin/MarkDuplicates.jar VALIDATION_STRINGENCY=SILENT I= "+barcode+".aligned.merged.bam O="+barcode+".aligned.duplicates_marked.bam M="+barcode+".aligned.bam.duplicates_marked.bam.duplicate_metrics TMP_DIR="+tmp_dir, farm_queue=farm, waitID=id3)
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cmd("java -jar /seq/software/picard/current/bin/CalculateHsMetrics.jar BI="+options.bait_list+" TI="+options.target_list+" I="+barcode+".aligned.duplicates_marked.bam M="+barcode+".hs_metrics VALIDATION_STRINGENCY=SILENT", farm_queue=farm, waitID = id4)
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fout = open("hybrid_selection.metrics", "w")
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print >> fout, "BARCODE\t"+get_line_number_from_file(barcodes[0]+".hs_metrics", 6).rstrip()
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for barcode in barcodes:
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print >> fout, barcode+"\t"+get_line_number_from_file(barcode+".hs_metrics", 7).rstrip()
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