oxpig / ANARCI

Antibody Numbering and Antigen Receptor ClassIfication
BSD 3-Clause "New" or "Revised" License
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Different species webapp vs python #40

Open SinelPan opened 2 years ago

SinelPan commented 2 years ago

Wrong species value when using Anarci python library (pip install anarci) compared to the webapp version,but CDRs are exactly the same. Please see below. For this sequence: IVFLLKGVQSEVKLEESGGGLVQPGGSMKLSCAASGFTFSDAWMDWVRQSPEKGLEWVAEIRNKANNHATYYDESVKGRFTISRDDSKSRVYLQMISLRAEDTGLYYCTGEFANWGQGTLVTVSA

Output from Webapp shows that species is "mouse".

Output from command line version shows that species is "human".

ANARCI -i IVFLLKGVQSEVKLEESGGGLVQPGGSMKLSCAASGFTFSDAWMDWVRQSPEKGLEWVAEIRNKANNHATYYDESVKGRFTISRDDSKSRVYLQMISLRAEDTGLYYCTGEFANWGQGTLVTVSA --scheme imgt
Input sequence
ANARCI numbered
Domain 1 of 1
Most significant HMM hit
|species|chain_type|e-value|score|seqstart_index|seqend_index|
|human|H|1.5e-52|168.2|10|124|
 Scheme = imgt

Output from the python library shows that species is "human".

aaseq = "IVFLLKGVQSEVKLEESGGGLVQPGGSMKLSCAASGFTFSDAWMDWVRQSPEKGLEWVAEIRNKANNHATYYDESVKGRFTISRDDSKSRVYLQMISLRAEDTGLYYCTGEFANWGQGTLVTVSA"
scheme = "imgt"
from anarci import anarci

n, x, _ = anarci(
    sequences=[("id0", aaseq)],
    scheme=scheme,
)
print(x)

[[{'id': 'human_H', 'description': '', 'evalue': 1.5e-52, 'bitscore': 168.2, 'bias': 0.2, 'query_start': 10, 'query_end': 124, 'species': 'human', 'chain_type': 'H', 'scheme': 'imgt', 'query_name': 'id0'}]]

Tested with python library version 1.3

pip list | grep anarci
anarci             1.3

and hmmscan version 3.3

hmmscan :: search sequence(s) against a profile database
HMMER 3.3 (Nov 2019); http://hmmer.org/
Copyright (C) 2019 Howard Hughes Medical Institute.
Freely distributed under the BSD open source license.
qiuqingpo commented 1 year ago

I meet the same problems. Any one who can help me? thank you!