def run_anarci(sequences): '''Run ANARCI annotation to get AHo numbering.''' allowed_species = 'human' allow = 'H' ncpu = 1 scheme = 'aho' numbered, alignment_details, hit_tables = anarci(sequences, scheme=scheme, output=False, allow=allow, ncpu=ncpu, allowed_species=allowed_species) return numbered
("12e8:H", "EVQLQQSGAEVVRSGASVKLSCTASGFNIKDYYIHWVKQRPEKGLEWIGWIDPEIGDTEYVPKFQGKATMTADTSSNTAYLQLSSLTSEDTAVYYCNAGHDYDRGRFPYWGQGTLVTVSAAKTTPPSVYPLAP" ), ("12e8:L", "DIVMTQSQKFMSTSVGDRVSITCKASQNVGTAVAWYQQKPGQSPKLMIYSASNRYTGVPDRFTGSGSGTDFTLTISNMQSEDLADYFCQQYSSYPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASV" ), ("scfv:A", "DIQMTQSPSSLSASVGDRVTITCRTSGNIHNYLTWYQQKPGKAPQLLIYNAKTLADGVPSRFSGSGSGTQFTLTISSLQPEDFANYYCQHFWSLPFTFGQGTKVEIKRTGGGGSGGGGSGGGGSGGGGSEVQLVESGGGLVQPGGSLRLSCAASGFDFSRYDMSWVRQAPGKRLEWVAYISSGGGSTYFPDTVKGRFTISRDNAKNTLYLQMNSLRAEDTAVYYCARQNKKLTWFDYWGQGTLVTVSSHHHHHH" ), ("lysozyme:A", "KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL" ) ] # Hand the list of sequences to the anarci function. Number them with the IMGT scheme results = anarci(sequences, scheme="imgt", output=False) # Unpack the results. We get three lists numbering, alignment_details, hit_tables = results # Each has the same number of elements as the number of sequences submitted assert len(numbering) == len(alignment_details) == len(hit_tables) == len( sequences) print( 'I am using the anarci function to number and get all the details about the following sequences' ) print(sequences) print('\n') # Iterate over the sequences