Olamide Isreal
8887cbe592
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41 lines
1.7 KiB
Python
41 lines
1.7 KiB
Python
from anarci import validate_sequence, anarci, scheme_short_to_long
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def number_single_sequence(sequence, chain, scheme="imgt", allowed_species=['human','mouse']):
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validate_sequence(sequence)
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try:
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if scheme != "raw":
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scheme = scheme_short_to_long[scheme.lower()]
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except KeyError:
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raise NotImplementedError(f"Unimplemented numbering scheme: {scheme}")
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assert len(sequence) > 70, f"Sequence too short to be an Ig domain. Please give whole sequence:\n{sequence}"
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allow = [chain]
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if chain == "L":
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allow.append("K")
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# Use imgt scheme for numbering sanity checks
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numbered, _, _ = anarci([("sequence", sequence)], scheme='imgt', output=False, allow=set(allow), allowed_species=allowed_species)
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assert numbered[0], f"Sequence provided as an {chain} chain is not recognised as an {chain} chain."
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output = [x for x in numbered[0][0][0] if x[1] != "-"]
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numbers = [x[0][0] for x in output]
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# Check for missing residues assuming imgt numbering
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assert (max(numbers) > 120) and (min(numbers) < 8), f"Sequence missing too many residues to model correctly. Please give whole sequence:\n{sequence}"
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# Renumber once sanity checks done
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if scheme == "raw":
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output = [((i+1, " "),x[1]) for i,x in enumerate(output)]
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elif scheme != 'imgt':
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numbered, _, _ = anarci([("sequence", sequence)], scheme=scheme, output=False, allow=set(allow), allowed_species=allowed_species)
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output = [x for x in numbered[0][0][0] if x[1] != "-"]
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return output
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def number_sequences(seqs, scheme="imgt", allowed_species=['human','mouse']):
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return {chain: number_single_sequence(seqs[chain], chain, scheme=scheme, allowed_species=allowed_species) for chain in seqs}
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