prihoda / abnumber Goto Github PK

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?

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 it didn't fix the error.

how to deal with the sequence with more than one variable domain, like scFv ?

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 solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed

UnsatisfiableError:

how to get v_identity, j_identity against with germline , of which a output of anarci if assign_germline ?

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 very much!

When we want to number multiple sequences, ANARCI takes an ncpu argument that allows running hmmer in parallel. Here it seems the Chain class can only take one sequence and send it to ANARCI. Would it be possible to have a wrapper class (e.g. Chains) that runs ANARCI in parallel?

Great work with this package! Interpreting the outputs of these is so much easier than those of ANARCI's.

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 by RHESG. May I ask why we see this change?

from abnumber import Chain

seq = "AVQLVDSGGGTLQAGKSLRLSCAISGLAFDGGAMGSEHRLTAGAMGWFRQAPGKDREFVAAISPRTDETYYAESLEGRFSVSRDAAATMVFLQADNVRLDDTASYYCAADEDVTPRVMGVIPHADHWGQGTLVTVSS"
chain = Chain(seq, scheme='imgt')
print("Sequence:\n", seq)
print("Chain:\n", chain)
assert chain.seq==seq

Thanks for your reply in advance

anarci supports 2 domains in one sequence, while abnumber does not

abnumber.exceptions.ChainParseError: Found 2 antibody domains in sequence: "DIQLTQSPSFLSASVGDRVTITCSARSSISFMYWYQQKPGKAPKLLIYDTSNLASGVPSRFSGSGSGTEFTLTISSLEAEDAATYYCQQWSSYPLTFGQGTKLEIKGGGSGGGGEVQLVESGGGLVQPGGSLRLSCAASGFTFSTYAMNWVRQAPGKGLEWVGRIRSKYNNYATYYADSVKDRFTISRDDSKNSLYLQMNSLKTEDTAVYYCVRHGNFGNSYVSWFAYWGQGTLVTVSSGGCGGGEVAALEKEVAALEKEVAALEKEVAALEKGGGDKTHTCPPCPAPEAAGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKISKAKGQPREPQVYTLPPSREEMTKNQVSLWCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK"