AbNumber
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prihoda
Convenience Python APIs for antibody numbering using ANARCI
Hi, Running the snippet below, I expected to see a similar `chain.seq` to the input sequence but it seems the order of amino acids is modified. Specifically `GSEHR` is replaced...
anarci supports 2 domains in one sequence, while abnumber does not abnumber.exceptions.ChainParseError: Found 2 antibody domains in sequence: "DIQLTQSPSFLSASVGDRVTITCSARSSISFMYWYQQKPGKAPKLLIYDTSNLASGVPSRFSGSGSGTEFTLTISSLEAEDAATYYCQQWSSYPLTFGQGTKLEIKGGGSGGGGEVQLVESGGGLVQPGGSLRLSCAASGFTFSTYAMNWVRQAPGKGLEWVGRIRSKYNNYATYYADSVKDRFTISRDDSKNSLYLQMNSLKTEDTAVYYCVRHGNFGNSYVSWFAYWGQGTLVTVSSGGCGGGEVAALEKEVAALEKEVAALEKEVAALEKGGGDKTHTCPPCPAPEAAGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKISKAKGQPREPQVYTLPPSREEMTKNQVSLWCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK"
Anarci is already able to do wolfguy labeling. By including the Scheme boarders abnumber can handle the annotation as well.
Added type annotations to a few classes where the argument type was ambiguous. Can add more if desired.
Hi , I downloaded AbNumber by conda, but when I used abnumber.Chain, I got the FileNotFoundError : No such file or directory: 'hmmscan'. I tried to install the hmmer, but...
I am trying to install this package as instructed but getting the following errors. C:\>conda install -c bioconda abnumber Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen...
Thank you for the great repo. I found AbNumber can print out the alignment with numberings. Can I get start and end number of CDR and framework as strings?
how to get v_identity, j_identity against with germline , of which a output of anarci if assign_germline ?
When we want to number multiple sequences, `ANARCI` [takes an `ncpu` argument](https://github.com/oxpig/ANARCI/blob/c2fd0f75ee3aa4cff842548d3d75b64815a8f663/lib/python/anarci/anarci.py#L857-L882) that allows running `hmmer` in parallel. [Here](https://github.com/prihoda/AbNumber/blob/b8d8d655eca6440d4b1bd8559f4a49ccfa408cf7/abnumber/common.py#L23-L31) it seems the `Chain` class can only take one sequence and...
Hello @prihoda, After `conda install` AbNumber (successfully), I tried to run the example from your documentation, but got an error:  Would you please help me with this? Thank you...
