From eb4b9a743ae4ea120d78378d96ca575b759a09ae Mon Sep 17 00:00:00 2001
From: andrewk <andrewk@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 31 Jul 2009 00:18:45 +0000
Subject: [PATCH] Script that runs most of the steps involved in validating the
 CoverageEval system that predicts performance for given depth of sequencing
 coverage across a genome.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1353 348d0f76-0448-11de-a6fe-93d51630548a
---
 python/CoverageMeta.py | 98 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 98 insertions(+)
 create mode 100755 python/CoverageMeta.py

diff --git a/python/CoverageMeta.py b/python/CoverageMeta.py
new file mode 100755
index 000000000..1371f6238
--- /dev/null
+++ b/python/CoverageMeta.py
@@ -0,0 +1,98 @@
+#!/usr/bin/python
+
+import sys, os
+from farm_commands import cmd
+
+#if __name__ == "__main__":
+from optparse import OptionParser
+class OptionParser (OptionParser):
+
+    def check_required (self, opts):
+        for opt in opts:
+            option = self.get_option(opt)
+
+            # Assumes the option's 'default' is set to None!
+            if getattr(self.values, option.dest) is None:
+                self.error("%s option not supplied" % option)
+
+def exists_and_non_zero(file):
+    return os.path.exists(file) and os.path.getsize(file) != 0
+
+# Global files
+gatk_exe = "java -Xmx8192m -jar ~/dev/Sting/trunk/dist/GenomeAnalysisTK.jar "
+ref = " -R /broad/1KG/reference/human_b36_both.fasta"
+
+parser = OptionParser()
+parser.add_option("-b", "--bam-file", help="Input BAM filename", dest="bam_file", default=None)
+
+(options, args) = parser.parse_args()
+parser.check_required(("-b",))    
+output_base = os.path.splitext(options.bam_file)[0]
+print "Input BAM file:",options.bam_file
+
+# Assure that hapmap chip file is here
+hapmapchip_file = output_base+".hapmapchip.gff"
+if not exists_and_non_zero(hapmapchip_file):
+    sys.exit("Expected to find "+hapmapchip_file+" but it's not around")
+
+# Run SSG calls
+ssg_outfile = output_base+".SSG.calls"
+if not exists_and_non_zero(ssg_outfile):
+    print "Running SingleSampleGenotyper"
+    Cmd = gatk_exe + ref + " -T SingleSampleGenotyper"+\
+        " -I "+options.bam_file+\
+        " -varout "+ssg_outfile+\
+        " -L 1"+\
+        " -fmq0 -l INFO "
+    cmd(Cmd)
+
+# Run VariantEval on SSG calls
+varianteval_outdir = "VariantEval"
+varianteval_outbase = "VariantEval/"+output_base
+varianteval_outfile = "VariantEval/"+output_base+".all.genotype_concordance"
+
+if not exists_and_non_zero(varianteval_outfile):
+    print "Running VarianteEval with output to "+varianteval_outbase
+    if not os.path.exists(varianteval_outdir):
+        os.mkdir(varianteval_outdir)
+    Cmd = gatk_exe + ref + "-T VariantEval"+\
+        " -B dbsnp,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod"+\
+        " -B eval,Variants,"+ssg_outfile+\
+        " -hc "+hapmapchip_file+\
+        " -o "+varianteval_outbase+\
+        " -L /humgen/gsa-scr1/andrewk/coverage/b36.hapmap_intervals.chr1"+\
+        " -evalContainsGenotypes"+\
+        " -minDiscoveryQ 5"+\
+        " -fmq0 -l INFO"
+    cmd(Cmd)
+
+# Run CoverageHist on BAM file
+hist_outfile = output_base+".hapmap.coverage_hist"
+if not exists_and_non_zero(hist_outfile):
+    print "Running CoverageHist on "+options.bam_file
+    Cmd = gatk_exe + ref + "-T CoverageHistogram"+\
+        " -I "+options.bam_file+\
+        " -o "+hist_outfile+\
+        " -L /humgen/gsa-scr1/andrewk/coverage/b36.hapmap_intervals.chr1"+\
+        " -fmq0 -l INFO"
+        #" -hc ~/coverage/NA12878.b36.gff"+\
+        #" -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod"+\ 
+        
+    cmd(Cmd)#,"gsa", output_base)
+
+# Now show CoverageEval predictions
+Cmd = "CoverageEval.py -e"+\
+    " -s /humgen/gsa-scr1/projects/1kg_pilot2/coverage_eval/fixed_stats/NA12878.CLEANED.chr1.full.hapmap.stats"+\
+    " -g "+hist_outfile
+cmd(Cmd)
+    
+
+    
+    
+    
+    
+    
+    
+    
+    
+    
\ No newline at end of file