import sys from cgData.matrix import GeneMatrix from cgData.sampleMap import SampleMap handle = open( sys.argv[1] ) sm = SampleMap() sm.read( handle ) handle.close() gmList = [] sampleHash = {} for path in sys.argv[2:]: gm = GeneMatrix() handle = open( path ) gm.readTSV( handle, skipVals=True ) handle.close() gmList.append( gm ) for sample in gm.getSampleList(): if sample not in sampleHash: sampleHash[ sample ] = [] sampleHash[ sample ].append( path ) sampleRemap = {} for sample in sampleHash: children = sm.getChildren( sample ) for c in children: if c in sampleHash: sampleRemap[ c ] = sample test = {}
#!/usr/bin/env python from cgData.matrix import GeneMatrix import sys handle = open(sys.argv[1]) gm = GeneMatrix() gm.readTSV(handle) gm.writeGCT(sys.stdout, missing="0")
#!/usr/bin/env python from cgData.matrix import GeneMatrix import sys handle = open( sys.argv[1] ) gm = GeneMatrix() gm.readTSV( handle ) gm.writeGCT( sys.stdout, missing="0" )