diff seg2matrix/CGData/GenomicMatrix.py @ 31:ab20c0d04f4a

add seg2matrix tool

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seg2matrix/CGData/GenomicMatrix.py	Fri Jul 24 13:10:11 2015 -0700
@@ -0,0 +1,37 @@
+
+import csv
+import CGData
+import CGData.BaseMatrix
+
+class GenomicMatrix(CGData.BaseMatrix.BaseMatrix):
+
+    __format__ = {
+            "name" : "genomicMatrix",
+            "type" : "type",
+            "form" : "matrix",
+            "rowType" : "probeMap",
+            "colType" : "idMap",
+            "valueType" : "float",
+            "nullString" : "NA",
+            "links" : {
+                "dataSubType" : {}
+            }
+        }    
+
+    def __init__(self):
+        CGData.BaseMatrix.BaseMatrix.__init__(self)
+
+    def init_blank(self, cols, rows):
+        super(GenomicMatrix, self).init_blank(cols=cols,rows=rows)
+        if 'cgdata' not in self:
+            self['cgdata'] = { 'type' : 'genomicMatrix' }
+
+    def get_probe_list(self):
+        return self.get_row_list()
+
+    def get_sample_list(self):
+        return self.get_col_list()
+    
+    def get_data_subtype(self):
+        return self.get('cgdata', {}).get('dataSubType', None)
+