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:
