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 = []