def testBarcodeFile(self):
del ERRORS[:]
del OUTPUT[:]
cysbar._writeError = _captureError
cysbar._writeOutput = _captureOutput
positions = [5]
barcodes = []
rc = cysbar.barcode("../data/test/seq1.fa", positions, barcodes, "../data/test/barcodes2.txt", residueSeparator)
self.assertEqual(rc, 0)
self.assertEqual(len(OUTPUT), 2)
self.assertEqual(OUTPUT[0], ">seq1__BC__Q__BC__")
self.assertEqual(OUTPUT[1], "RDESabc123SHKFKGTIR---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.barcode("../data/test/seq1.fa", positions, barcodes, None, residueSeparator)
self.assertEqual(rc, 0)
self.assertEqual(len(OUTPUT), 2)
self.assertEqual(OUTPUT[0], ">seq1__BC__Q__BC__")
self.assertEqual(OUTPUT[1], "RDESwwyhwyyhmmSHKFKGTIR---XSNRDCESQSHKFKGTCIR---XSNCASVCXS-E-GF--NGGHCRG--RRCYCTAK-")