Refactored so it could be used for knownGene and CCDS as well as refGene
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3373 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
weisburd
parent
35b4bba35e
commit
04e14ef85a
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@ -5,17 +5,16 @@ import traceback
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from optparse import OptionParser, OptionGroup
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from IndentedHelpFormatterWithNL import *
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run_locally = True
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# Init cmd-line args
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description = """
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This script runs a command that concatenates all 50 results of the GenerateTranscriptToInfo.py script into one big file that can be directly used by the GenomicAnnotator.
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This script runs a command that concatenates all 50 per-chromosome files generated by the GenerateTranscriptToInfo.py script into one big file that can be directly used by the GenomicAnnotator.
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"""
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parser = OptionParser( description=description, usage="usage: %prog [options] ", formatter=IndentedHelpFormatterWithNL())
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parser.add_option("-r", "--refgene-directory", metavar="DIR", dest="refgene_dir", help="Specifies the directory that contains refGene-converted.txt", default="/humgen/gsa-hpprojects/GATK/data/Annotations/refseq/raw/")
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parser.add_option("-d", "--directory", metavar="DIR", dest="directory", help="Specifies the directory that contains the files to concatenate (eg. /humgen/gsa-hpprojects/GATK/data/Annotations/refseq/raw/)")
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parser.add_option("-f", "--filename-prefix", metavar="PREFIX", dest="prefix", help="Filename prefix (eg. refGene)")
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parser.add_option("-u", "--ucsc", dest="ucsc", action="store_true", default=False, help="Generate the output file for use with the NCBI reference genome (this effects chromosome order and naming (eg. M chromosome is first and its called 'chrM' instead of 'MT')).")
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parser.add_option("-n", "--ncbi", dest="ncbi", action="store_true", default=False, help="Generate the output file for use with the UCSC reference genome (this effects chromosome order and naming (eg. MT chromosome is last and its called 'MT' instead of 'chrM')).")
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@ -33,6 +32,13 @@ ncbi = options.ncbi
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if not ucsc and not ncbi:
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error("Must run with either -u or -n")
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directory = options.directory
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if not directory:
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error("Must specify the directory using -d")
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prefix = options.prefix
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if not prefix:
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error("Must specify filename prefix using -f")
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contig_chars = []
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if ucsc:
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@ -49,30 +55,30 @@ if ucsc: # NCBI doesn't have the _random contigs
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#print(contigs)
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dir_plus_prefix = os.path.join(directory,prefix)
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# Update the refGene-big-table-header.txt header file using the header from one of the single-contig files.
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command = "head -n 1 " + (options.refgene_dir + "/refGene-big-table-ucsc-%s.txt " % contigs[0]) + " > " + options.refgene_dir + "/refGene-big-table-header.txt"
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print(command)
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os.system(command)
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# Update the *-big-table-header.txt header file using the header from one of the single-contig files.
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#command = "head -n 1 " + dir_plus_prefix + ("-big-table-ucsc-%s.txt " % contigs[0]) + " > " + dir_plus_prefix + "-big-table-header.txt"
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#print(command)
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#os.system(command)
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# Concatenate
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header_start = open(options.refgene_dir+"/refGene-big-table-header.txt").read().split("\t")[0]
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header_start = open(dir_plus_prefix + "-big-table-header.txt").read().split("\t")[0]
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command = "cat "
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for contig in contigs:
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command += options.refgene_dir+"/refGene-big-table-ucsc-%s.txt " % contig
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command += dir_plus_prefix + "-big-table-ucsc-%s.txt " % contig
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command += " | grep -v " + header_start
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if ncbi:
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command += "| perl -pe 's/^chrM(.*)$/MT\\1/i' | perl -pe 's/^chr([^p].*)$/\\1/i' " # rename chrM to MT and remove the 'chr' from chromosome names
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command += " | cat " + options.refgene_dir+"/refGene-big-table-header.txt - "
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command += " | cat " + dir_plus_prefix + "-big-table-header.txt - "
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if ucsc:
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command += " > " + options.refgene_dir+"/refGene-big-table-ucsc.txt"
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command += " > " + dir_plus_prefix + "-big-table-ucsc.txt"
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else:
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command += " > " + options.refgene_dir+"/refGene-big-table-ncbi.txt"
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command += " > " + dir_plus_prefix + "-big-table-ncbi.txt"
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print(command)
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os.system(command)
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@ -5,22 +5,25 @@ import traceback
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from optparse import OptionParser, OptionGroup
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from IndentedHelpFormatterWithNL import *
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run_locally = False
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# Init cmd-line args
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description = """
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This script submits LSF jobs that run the GATK TranscriptToInfo Walker on each individual chromosome. This reduces the overall runtime to a managable ammount (eg. < 1 day).
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This script submits LSF jobs that run the GATK TranscriptToInfo Walker on each individual chromosome. This reduces the overall runtime to a manageable ammount (eg. < 1 day).
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NOTE: This script must be run in the top level dir of your GATK checkout area.
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"""
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parser = OptionParser( description=description, usage="usage: %prog [options] ", formatter=IndentedHelpFormatterWithNL())
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parser.add_option("-d", "--refgene-directory", metavar="DIR", dest="refgene_dir", help="Specifies the directory that contains refGene-converted.txt", default="/humgen/gsa-hpprojects/GATK/data/Annotations/refseq/hg18_b36/raw/")
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parser.add_option("-p", "--print", dest="output", action="store_true", default=False, help="Only print the commands to standard out, don't actually execute them yet.")
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parser.add_option("-i", "--transcript-table", metavar="PATH", dest="transcript_table", help="Path of the file that contains the transcript data in AnnotatorROD format (eg. /humgen/gsa-hpprojects/GATK/data/Annotations/refseq/raw/refGene-converted.txt)")
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parser.add_option("-f", "--output-filename-prefix", metavar="PREFIX", dest="prefix", help="Output filename prefix (eg. refGene)")
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parser.add_option("-p", "--print", dest="justprint", action="store_true", default=False, help="Only print the commands to standard out, don't actually execute them yet.")
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parser.add_option("-e", "--execute", dest="execute", action="store_true", default=False, help="Executes the commands. This flag acts as a confirmation that you want to proceed with launching the processes.")
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parser.add_option("-l", "--locally", dest="run_locally", action="store_true", default=False, help="Don't submit the commands to LSF. Run them sequentially on the current machine.")
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parser.add_option("-R", "--reference", metavar="PATH", dest="reference", help="Specifies the path of the reference file to use.", default="/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")
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parser.add_option("-n", "--gene-name-columns", dest="gene_name_columns", metavar="GENE_NAMES", help="Comma-separated list of column names that contain gene names. This arg is passed through to the GenomicAnnotator. The GenomicAnnotator docs have more details on this.")
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parser.add_option("-q", "--queue", dest="queue", metavar="QUEUE", help="Specifies the LSF queue to use.", default="solexa")
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(options, args) = parser.parse_args()
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@ -30,14 +33,32 @@ def error(msg):
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sys.exit(-1)
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run = options.execute
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output = options.output
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justprint = options.justprint
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run_locally = options.run_locally
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if not run and not output:
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if not run and not justprint:
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error("Must run with either -p or -e")
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transcript_table = options.transcript_table
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if not transcript_table or not os.access(transcript_table, os.R_OK):
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error("Must specify a valid transcript table file path using -i")
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gene_name_columns = options.gene_name_columns
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if not gene_name_columns:
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error("Must specify gene name columns using -n")
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output_file_prefix = options.prefix
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if not output_file_prefix:
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error("Must specify the output file prefix using -f")
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reference = options.reference
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if not os.access(reference, os.R_OK):
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error("Couldn't access reference file: "+ reference)
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queue = options.queue
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transcript_dir = os.path.dirname(transcript_table)
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logs_dir = os.path.join(transcript_dir,"logs")
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contig_chars = ["M"] + range(1,23) + ["X", "Y"]
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@ -45,29 +66,32 @@ contigs = []
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contigs += [ "chr" + str(x) for x in contig_chars ]
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contigs += [ "chr" + str(x) + "_random" for x in set( contig_chars ).difference(set(['M',12,14,20,'X','Y'])) ] # There are no "_random" chromosomes for chrM,12,14,20,Y
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#print(contigs)
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if run:
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print("Deleting any previous logs...")
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os.system("rm " + options.refgene_dir+"/logs/bsub_*_log.txt")
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for contig in contigs:
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os.system("rm " + os.path.join(logs_dir,"bsub_*_log.txt"))
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os.system("mkdir " + logs_dir)
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for contig in contigs:
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if contig.count("random") or contig.lower().count("chrm"):
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MEMORY_USAGE = 10 #Gigabytes
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MEMORY_USAGE = 10 # Gigabytes
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EXCLUSIVE = ""
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else:
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if run_locally:
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MEMORY_USAGE = 32
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MEMORY_USAGE = 64
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else:
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MEMORY_USAGE = 15
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MEMORY_USAGE = 32
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EXCLUSIVE = ""
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command = "java -Xmx"+str(MEMORY_USAGE)+"g -jar dist/GenomeAnalysisTK.jar -T TranscriptToInfo -l info -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -B refgene,AnnotatorInputTable,"+options.refgene_dir+"/refGene-converted.txt -o "+options.refgene_dir+"/refGene-big-table-ucsc-%s.txt -L %s:1+ " % (contig, contig)
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#print(command)
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if not run_locally:
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command = "bsub "+EXCLUSIVE+" -q solexa -R \"rusage[mem="+str(MEMORY_USAGE)+"]\" -o "+options.refgene_dir+"/logs/bsub_"+contig+"_log.txt "+command
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command = "java -Xmx"+str(MEMORY_USAGE)+"g -jar dist/GenomeAnalysisTK.jar -T TranscriptToInfo -l info -R " + reference + " -B transcripts,AnnotatorInputTable,"+transcript_table+" -n "+gene_name_columns+" -o "+ os.path.join(transcript_dir,output_file_prefix) +"-big-table-ucsc-%s.txt -L %s:1+ " % (contig, contig)
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if run_locally:
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command += " > " + os.path.join(logs_dir,contig+"_log.txt")
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else:
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command = "bsub "+EXCLUSIVE+" -q " + queue + " -R \"rusage[mem="+str(MEMORY_USAGE)+"]\" -o " + os.path.join(logs_dir,contig+"_log.txt") + " " + command
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if run:
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print("Executing: " + command)
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