Comments (5)
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)?
from gget.
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'
from gget.
from gget.
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.
from gget.
thank you.
from gget.
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from gget.