def FASTA_alignment():
# example for talk
f = FASTA.retrieve('1YGV', cache_dir) + FASTA.retrieve('3HQV', cache_dir)
sa = SequenceAligner.from_FASTA(f)
print(sa)
uparcA = sa.get_uniparc_object('A')
sys.exit(0)
cache_dir = '/home/oconchus/temp'
pdb_id = '1KI1'
uniparc_sequences = {}
pdb_uniparc_mapping = pdb_to_uniparc(['1KI1'], cache_dir = cache_dir)
for upe in pdb_uniparc_mapping['1KI1']:
uniparc_sequences[upe.UniParcID] = upe.sequence
f = FASTA.retrieve('1KI1', cache_dir = cache_dir)
f = f['1KI1']
chains = sorted(f.keys())
for uniparc_id, uniparc_sequence in uniparc_sequences.iteritems():
print(uniparc_sequence)
chain_matches = {}
for c in chains:
chain_matches[c] = []
colortext.message("MATCHING CHAIN C")
fasta_sequence = f[c]
string_matches = []
