57 lines
1.9 KiB
Python
57 lines
1.9 KiB
Python
|
import sys
|
||
|
|
import os
|
||
|
|
import re
|
||
|
|
import traceback
|
||
|
|
from optparse import OptionParser, OptionGroup
|
||
|
|
from IndentedHelpFormatterWithNL import *
|
||
|
|
|
||
|
|
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.
|
||
|
|
"""
|
||
|
|
|
||
|
|
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/")
|
||
|
|
|
||
|
|
(options, args) = parser.parse_args()
|
||
|
|
|
||
|
|
def error(msg):
|
||
|
|
print("ERROR: %s. (Rerun with -h to print help info) \n" % msg)
|
||
|
|
#parser.print_help()
|
||
|
|
sys.exit(-1)
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
contig_chars = ["M"] + range(1,23) + ["X", "Y"]
|
||
|
|
|
||
|
|
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
|
||
|
|
|
||
|
|
#print(contigs)
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
# Update the refGene-big-table-header.txt header file using the header from one of the single-contig files.
|
||
|
|
command = "head -n 1 " + (options.refgene_dir + "/refGene-big-table-ucsc-%s.txt " % contigs[0]) + " > " + options.refgene_dir + "/refGene-big-table-header.txt"
|
||
|
|
print(command)
|
||
|
|
os.system(command)
|
||
|
|
|
||
|
|
|
||
|
|
# Concatenate
|
||
|
|
header_start = open(options.refgene_dir+"/refGene-big-table-header.txt").read().split("\t")[0]
|
||
|
|
command = "cat "
|
||
|
|
for contig in contigs:
|
||
|
|
command += options.refgene_dir+"/refGene-big-table-ucsc-%s.txt " % contig
|
||
|
|
|
||
|
|
command += " | grep -v " + header_start
|
||
|
|
command += " | cat " + options.refgene_dir+"/refGene-big-table-header.txt - "
|
||
|
|
|
||
|
|
command += " > " + options.refgene_dir+"/refGene-big-table-ucsc.txt"
|
||
|
|
print(command)
|
||
|
|
os.system(command)
|
||
|
|
|