Keyerror: "0000:query" about gget

[lauraluebbert]

Hi, thanks for using gget and for reaching out. Which gget version are you using? Could you please send me your exact command (including the sequence)?

[sharzil1994]

thank you for your response.

• I used the given command to install package around two weeks prior
  pip install --upgrade gget
• however i can't seem to find the installed version
  -I used the given example that worked fine that is
  import gget
  gget.setup("alphafold") # setup only needs to be run once
  gget.alphafold("MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK")
• however it gives issue when is use
  gget.alphafold("MVKVFLVDDHEVVRRGLVDLLGADPELDVVGEAGSVAEAMARVPAARPDVAVLDVRLPDGNGIELCRDLLSRMPDLRCLILTSYTSDEAMLDAILAGASGYVVKDIKGMELARAVKDVGAGRSLLDNRAAAALMAKLRGAAEKQDPLSGLTDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQAAVFATELKRSRPPGDGP")

-the error is

KeyError Traceback (most recent call last)
/tmp/ipykernel_10534/2425348286.py in
1 import gget
----> 2 gget.alphafold("MVKVFLVDDHEVVRRGLVDLLGADPELDVVGEAGSVAEAMARVPAARPDVAVLDVRLPDGNGIELCRDLLSRMPDLRCLILTSYTSDEAMLDAILAGASGYVVKDIKGMELARAVKDVGAGRSLLDNRAAAALMAKLRGAAEKQDPLSGLTDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQAAVFATELKRSRPPGDGP")

~/anaconda3/envs/openmm/lib/python3.7/site-packages/gget/gget_alphafold.py in alphafold(sequence, out, relax, plot, show_sidechains)
485 for db_name, db_results in raw_msa_results.items():
486 merged_msa = notebook_utils.merge_chunked_msa(
--> 487 results=db_results, max_hits=MAX_HITS.get(db_name)
488 )
489 if merged_msa.sequences and db_name != "uniprot":

~/anaconda3/envs/openmm/lib/python3.7/site-packages/alphafold/notebooks/notebook_utils.py in merge_chunked_msa(results, max_hits)
105 e_values_dict = parsers.parse_e_values_from_tblout(chunk['tbl'])
106 # Jackhmmer lists sequences as /-.
--> 107 e_values = [e_values_dict[t.partition('/')[0]] for t in msa.descriptions]
108 chunk_results = zip(
109 msa.sequences, msa.deletion_matrix, msa.descriptions, e_values)

~/anaconda3/envs/openmm/lib/python3.7/site-packages/alphafold/notebooks/notebook_utils.py in (.0)
105 e_values_dict = parsers.parse_e_values_from_tblout(chunk['tbl'])
106 # Jackhmmer lists sequences as /-.
--> 107 e_values = [e_values_dict[t.partition('/')[0]] for t in msa.descriptions]
108 chunk_results = zip(
109 msa.sequences, msa.deletion_matrix, msa.descriptions, e_values)

KeyError: '0000|query'

[sharzil1994]

[lauraluebbert]

Oddly, the same error occurs when plugging this sequence into the original Alphafold Colab and hence it is not a problem with the gget implementation. I’ll let them know and continue to trouble-shoot.

[sharzil1994]

thank you.