From c214056d884edc405e946e5d66b9085e4d1bcf4a Mon Sep 17 00:00:00 2001
From: weisburd <weisburd@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 30 Apr 2010 15:47:08 +0000
Subject: [PATCH] Script for concatenating results of
 GenerateTranscriptToInfo.py into one big file

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3279 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../ConcatTranscriptToInfoResults.py          | 56 +++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100755 python/genomicAnnotatorScripts/ConcatTranscriptToInfoResults.py

diff --git a/python/genomicAnnotatorScripts/ConcatTranscriptToInfoResults.py b/python/genomicAnnotatorScripts/ConcatTranscriptToInfoResults.py
new file mode 100755
index 000000000..73c3b9f97
--- /dev/null
+++ b/python/genomicAnnotatorScripts/ConcatTranscriptToInfoResults.py
@@ -0,0 +1,56 @@
+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)
+