From 0069cb426d1d555678b0276dacb6e938687cfbc6 Mon Sep 17 00:00:00 2001
From: weisburd <weisburd@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 30 Apr 2010 15:27:52 +0000
Subject: [PATCH] Script for spawning LSF jobs that run the
 TranscriptToInfo.java walker on each of the 50 contigs.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3277 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../GenerateTranscriptToInfo.py               | 76 +++++++++++++++++++
 1 file changed, 76 insertions(+)
 create mode 100755 python/genomicAnnotatorScripts/GenerateTranscriptToInfo.py

diff --git a/python/genomicAnnotatorScripts/GenerateTranscriptToInfo.py b/python/genomicAnnotatorScripts/GenerateTranscriptToInfo.py
new file mode 100755
index 000000000..087c552ed
--- /dev/null
+++ b/python/genomicAnnotatorScripts/GenerateTranscriptToInfo.py
@@ -0,0 +1,76 @@
+import sys
+import os
+import re
+import traceback
+from optparse import OptionParser, OptionGroup
+from IndentedHelpFormatterWithNL import *
+
+run_locally = False
+
+# Init cmd-line args
+description = """
+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).
+
+NOTE: This script must be run in the top level dir of your GATK checkout area.
+"""
+
+parser = OptionParser( description=description, usage="usage: %prog [options] ", formatter=IndentedHelpFormatterWithNL())
+
+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/raw/")
+
+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.")
+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.")
+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.")
+
+(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)
+
+run = options.execute
+output = options.output
+run_locally = options.run_locally
+
+if not run and not output: 
+    error("Must run with either -p or -e")    
+
+
+
+
+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 are no "_random" chromosomes for chrM,12,14,20,Y
+
+#print(contigs)
+
+
+if run:
+    print("Deleting any previous logs...")
+    os.system("rm " + options.refgene_dir+"/logs/bsub_*_log.txt")
+for contig in contigs:
+        
+    if contig.count("random") or contig.lower().count("chrm"):
+        MEMORY_USAGE = 10  #Gigabytes
+        EXCLUSIVE = ""
+    else:
+        if run_locally:
+            MEMORY_USAGE = 32
+        else:
+            MEMORY_USAGE = 15
+        EXCLUSIVE = ""
+            
+    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)
+        #print(command)
+    if not run_locally:
+        command = "bsub "+EXCLUSIVE+" -q solexa -R \"rusage[mem="+str(MEMORY_USAGE)+"]\" -o "+options.refgene_dir+"/logs/bsub_"+contig+"_log.txt "+command
+    
+    
+    if run:
+        print("Executing: " + command)
+        os.system(command)
+    else:
+        print(command)