src/hg/tcga/scripts/processData.py 1.10

Index: src/hg/tcga/scripts/processData.py
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/tcga/scripts/processData.py,v
retrieving revision 1.9
retrieving revision 1.10
diff -b -B -U 4 -r1.9 -r1.10
--- src/hg/tcga/scripts/processData.py	12 Aug 2009 05:05:24 -0000	1.9
+++ src/hg/tcga/scripts/processData.py	12 Sep 2009 01:39:07 -0000	1.10
@@ -25,8 +25,9 @@
     print "\t\tuncOVG4502  -- Agilent G4502 Ovarian"
     print "\t\tharvardOVCGH415 -- Agilent G4124A 415K CGH Ovarian"
     print "\t\tuncOVMiRNA -- Agilent MiRNA Ovarian"
     print "\t\tjhuMethylOV -- Methylation27 Ovarian"
+    print "\t\trnaSeqOV -- RNA Seq DGE Ovarian"
     print ""
     
 def handleOpts(argv):
     opts, args = getopt.getopt(argv, "ht:", ["help", "type="])
@@ -93,18 +94,18 @@
         
     elif type == "harvard":
         baseDir = "/data/TCGA/O_harvardCGH/working/"
         patterns = ["*data.txt"]
-        bed12file = baseDir + "agilentCGH244A.bed"
+        bed12file = baseDir + "agilentCgh244a_bed12.bed"
         bed15file = baseDir + "harvardCGH244A_bed15.bed"
         prefix = "harvardCGH"
         
         Data = CGH244A(baseDir, patterns, bed12file, bed15file, prefix)
 
     elif type == "harvardOV":
         baseDir = "/data/TCGA/O_harvardOVCGH/working/"
         patterns = ["*.data.txt"]
-        bed12file = baseDir + "agilentCGH244A.bed"
+        bed12file = baseDir + "agilentCgh244a_bed12.bed"
         bed15file = baseDir + "harvardOVCGH244A_bed15.bed"
         prefix = "harvardOVCGH"
         
         Data = CGH244A(baseDir, patterns, bed12file, bed15file, prefix)
@@ -140,9 +141,9 @@
         
     elif type == "mskcc":
         baseDir = "/data/TCGA/O_mskccCGH/working/"
         patterns = ["*data.txt"]
-        bed12file = baseDir + "agilentCGH244A.bed"
+        bed12file = baseDir + "agilentCgh244a_bed12.bed"
         bed15file = baseDir + "mskccCGH244A_bed15.bed"
         prefix = "mskccCGH"
         
         Data = CGH244A(baseDir, patterns, bed12file, bed15file, prefix)
@@ -195,8 +196,18 @@
         prefix = "broadSNP6"
         
         Data = SNP6(baseDir, patterns, bed12file, bed15file, prefix)
 
+    elif type == "rnaSeqOV":
+        baseDir = "/data/TCGA/O_rnaSeqOV/working/"
+        patterns = ["*genes.txt"]
+        bed12file = baseDir + "rnaSeq32samples.bed"
+        bed15file = baseDir + "rnaSeqOV_bed15.bed"
+        prefix = "rnaSeqOV"
+        
+        Data = RNASeq(baseDir, patterns, bed12file, bed15file, prefix)
+        Data.medianNormalize = 1
+        
     elif type == "broadABI":
         baseDir = "/data/TCGA/C_broadABI/working/"
         patterns = ["*.maf"]
         bed12file = ""
@@ -227,9 +238,9 @@
     elif type == "broadOVABI":
         baseDir = "/data/TCGA/C_broadOVABI/working/"
         patterns = ["*.maf"]
         bed12file = ""
-        bed15file = baseDir + "broadOVSNP6_bed15.bed"
+        bed15file = baseDir + "broadOVABI_bed15.bed"
         prefix = "broadOVABI"
 
         Data = ABI(baseDir, patterns, bed12file, bed15file, prefix)
 
@@ -284,9 +295,9 @@
                                       "Nonsense_Mutation", "Missense_Mutation", "Missense",
                                       "Nonsense"]  
 
     elif type == "baylorOVABI":
-        baseDir = "/data/TCGA/OV/mutation/hgsc.bcm.edu_OV.ABI.1.1.0/"
+        baseDir = "/data/TCGA/C_baylorOVABI/working/"
         patterns = ["*.maf"]
         bed12file = ""
         bed15file = baseDir + "baylorOVABI_bed15.bed"
         prefix = "hgscOVABI"