def testTCGAMAFAsInput(self): """ Test that we can take in a TCGA MAF (using MAFLITE), do no annotations, and still render it properly """ tmp = MafliteInputMutationCreator("testdata/maf/Patient0.maf.annotated", 'configs/maflite_input.config') muts = tmp.createMutations() outputFilename = "out/testTCGAMAFAsInput.tsv" outputRenderer = TcgaMafOutputRenderer(outputFilename, 'configs/tcgaMAF2.4_output.config') outputRenderer.renderMutations(muts, tmp.getComments())
def testTCGAMAFAsInput(self): """ Test that we can take in a TCGA MAF (using MAFLITE), do no annotations, and still render it properly """ tmp = MafliteInputMutationCreator( "testdata/maf/Patient0.maf.annotated", None, 'configs/maflite_input.config') muts = tmp.createMutations() outputFilename = "out/testTCGAMAFAsInput.tsv" outputRenderer = TcgaMafOutputRenderer( outputFilename, 'configs/tcgaMAF2.4_output.config') outputRenderer.renderMutations(muts, tmp.getComments())