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Added option to generate UCSC or NCBI sequence 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3283 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
weisburd 2010-04-30 17:26:00 +00:00
parent 0e10359a5e
commit 28f746b76a
1 changed files with 28 additions and 5 deletions
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33
python/genomicAnnotatorScripts/ConcatTranscriptToInfoResults.py
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@ -9,27 +9,43 @@ run_locally = True
# Init cmd-line args
description = """
This script creates and runs the command line that concatenates all 50 results of the GenerateTranscriptToInfo.py script into one big file that can be directly used with the GenomicAnnotator.
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.
"""
parser = OptionParser( description=description, usage="usage: %prog [options] ", formatter=IndentedHelpFormatterWithNL())
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/")
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')).")
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')).")
(options, args) = parser.parse_args()
def error(msg):
print("ERROR: %s. (Rerun with -h to print help info) \n" % msg)
#parser.print_help()
parser.print_help()
sys.exit(-1)
ucsc = options.ucsc
ncbi = options.ncbi
if not ucsc and not ncbi:
error("Must run with either -u or -n")
contig_chars = ["M"] + range(1,23) + ["X", "Y"]
contig_chars = []
if ucsc:
contig_chars = ["M"] + range(1,23) + ["X", "Y"]
else:
contig_chars = range(1,23) + ["X", "Y", "M"]
contigs = []
contigs += [ "chr" + str(x) for x in contig_chars ]
contigs += [ "chr" + str(x) + "_random" for x in set( contig_chars ).difference(set(['M',12,14,20,'X','Y'])) ] # There's no _random chromosomes for chrM,12,14,20,Y
if ucsc: # NCBI doesn't have the _random contigs
contigs += [ "chr" + str(x) + "_random" for x in set( contig_chars ).difference(set(['M','MT',12,14,20,'X','Y'])) ] # There's no _random chromosomes for chrM,12,14,20,Y
#print(contigs)
@ -48,9 +64,16 @@ for contig in contigs:
command += options.refgene_dir+"/refGene-big-table-ucsc-%s.txt " % contig
command += " | grep -v " + header_start
if ncbi:
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
command += " | cat " + options.refgene_dir+"/refGene-big-table-header.txt - "
command += " > " + options.refgene_dir+"/refGene-big-table-ucsc.txt"
if ucsc:
command += " > " + options.refgene_dir+"/refGene-big-table-ucsc.txt"
else:
command += " > " + options.refgene_dir+"/refGene-big-table-ncbi.txt"
print(command)
os.system(command)