def test_read_fasta(self): headers, sequences = PB.read_fasta("test_data/1BTA.pdb.PB.fasta") self.assertEqual(headers, ["test_data/1BTA.pdb | chain A"]) self.assertEqual( sequences, ["ZZdddfklonbfklmmmmmmmmnopafklnoiakl" "mmmmmnoopacddddddehkllmmmmngoilmmmm" "mmmmmmmmnopacdcddZZ"], )
else: index_first_frame = options.first_frame-1 #------------------------------------------------------------------------------- # check input files #------------------------------------------------------------------------------- for name in options.f: if not os.path.isfile(name): sys.exit("%s does not appear to be a valid file.\nBye" % name) #------------------------------------------------------------------------------- # read PBs files #------------------------------------------------------------------------------- pb_seq = [] for name in options.f: pb_seq += PB.read_fasta(name)[1][index_first_frame:] #------------------------------------------------------------------------------- # check all sequences have the same size #------------------------------------------------------------------------------- pb_seq_size = len(pb_seq[0]) for seq in pb_seq: if len(seq) != pb_seq_size: sys.exit("cannot compute PB frequencies / different sequence lengths") #------------------------------------------------------------------------------- # count PBs at each position of the sequence #------------------------------------------------------------------------------- pb_count = numpy.zeros((pb_seq_size, len(PB.NAMES))) for seq in pb_seq: