src/hg/tcga/scripts/processData.py 1.7

Index: src/hg/tcga/scripts/processData.py
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/tcga/scripts/processData.py,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 4 -r1.6 -r1.7
--- src/hg/tcga/scripts/processData.py	17 Nov 2008 05:23:17 -0000	1.6
+++ src/hg/tcga/scripts/processData.py	25 Apr 2009 02:17:38 -0000	1.7
@@ -203,8 +203,40 @@
                                       "Splice_Site_SNP", "Splice_site",
                                       "Nonsense_Mutation", "Missense_Mutation", "Missense",
                                       "Nonsense"]  
 
+    elif type == "baylorOVABI":
+        baseDir = "/data/TCGA/OV/mutation/hgsc.bcm.edu_OV.ABI.1.1.0/"
+        patterns = ["*.maf"]
+        bed12file = ""
+        bed15file = baseDir + "baylorOVABI_bed15.bed"
+        prefix = "hgscOVABI"
+
+        Data = ABI(baseDir, patterns, bed12file, bed15file, prefix)
+
+        Data.bed12Files = []
+        Data.chromField = "CHROM"
+        Data.startField = "START_POSITION"
+        Data.stopField = "END_POSITION"
+        Data.strandField = "STRAND"
+        Data.statusField = "MUTATION_STATUS"
+        Data.classField = "VARIANT_CLASSIFICATION"
+        Data.sampleIdField = "TUMOR_SAMPLE_ID"
+
+        Data.collapseStatus = {}
+        Data.collapseStatus["Somatic"] = ["Somatic", '"somatic, homozygous"',
+                                          '"somatic, heterozygous"']
+        Data.collapseStatus["Germline"] = ["Germline", "LOH", "Unknown", "germline"]
+        
+        Data.collapseClass = {}
+        Data.collapseClass["Quiet"] = ["Silent", "Targeted_Region", "Synonymous"]
+        Data.collapseClass["Loud"] = ["frame_shift", "Frame_Shift_Del", "Frame_Shift_Ins",
+                                      "in_frame_insertion", "in_frame_deletion",
+                                      "In_Frame_Del", "In_Frame_Ins", "Splice_Site_Indel",
+                                      "Splice_Site_SNP", "Splice_site",
+                                      "Nonsense_Mutation", "Missense_Mutation", "Missense",
+                                      "Nonsense"]  
+
     elif type == "wustlABI":
         baseDir = "/data/TCGA/C_wustlABI/working/"
         patterns = ["*.maf"]
         bed12file = ""