def testBarcodeFile(self): del ERRORS[:] del OUTPUT[:] cysbar._writeError = _captureError cysbar._writeOutput = _captureOutput positions = [5] barcodes = [] rc = cysbar.reconstruct(["../data/test/seq1_pos5abc123.fa"], positions, barcodes, "../data/test/barcodes2.txt", None, residueSeparator, None) self.assertEqual(rc, 0) self.assertEqual(len(OUTPUT), 2) self.assertEqual(OUTPUT[0], ">seq1") self.assertEqual(OUTPUT[1], "RDESQSHKFKGTIR---XSNRDCESQSHKFKGTCIR---XSNCASVCXS-E-GF--NGGHCRG--RRCYCTAK-")
def testBarcodeParams(self): del ERRORS[:] del OUTPUT[:] cysbar._writeError = _captureError cysbar._writeOutput = _captureOutput positions = [5] barcodes = BUILT_IN_BARCODES[:1] rc = cysbar.reconstruct(["../data/test/seq1_pos5wwyhwyyhmm.fa"], positions, barcodes, None, None, residueSeparator, None) self.assertEqual(rc, 0) self.assertEqual(len(OUTPUT), 2) self.assertEqual(OUTPUT[0], ">seq1") self.assertEqual(OUTPUT[1], "RDESQSHKFKGTIR---XSNRDCESQSHKFKGTCIR---XSNCASVCXS-E-GF--NGGHCRG--RRCYCTAK-")