Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Different species webapp vs python #40

Open
SinelPan opened this issue Jul 22, 2022 · 1 comment
Open

Different species webapp vs python #40

SinelPan opened this issue Jul 22, 2022 · 1 comment

Comments

@SinelPan
Copy link

SinelPan commented Jul 22, 2022

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
Copy link

qiuqingpo commented Jul 28, 2023

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants