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Incorrect parsing of NCBI protein version accession #129

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HobnobMancer opened this issue May 20, 2024 · 1 comment · May be fixed by #130
Open

Incorrect parsing of NCBI protein version accession #129

HobnobMancer opened this issue May 20, 2024 · 1 comment · May be fixed by #130
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bug Something isn't working enhancement New feature or request

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@HobnobMancer
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cazy_webscraper is not identifying the NCBI protein version accessions correctly, and is unable to pair up the downloaded data with data in the local CAZyme database.

Traceback (most recent call last):
  File "/cazy_env/bin/cw_get_genbank_seqs", line 8, in <module>
    sys.exit(main())
  File "/cazy_env/lib/python3.6/site-packages/cazy_webscraper/expand/genbank/sequences/get_genbank_sequences.py", line 164, in main
    args,
  File "/cazy_env/lib/python3.6/site-packages/cazy_webscraper/expand/genbank/sequences/get_genbank_sequences.py", line 321, in get_seqs_from_ncbi
    args,
  File "/cazy_env/lib/python3.6/site-packages/cazy_webscraper/expand/genbank/sequences/get_genbank_sequences.py", line 534, in parse_failed_connections
    failed_connections_batches["_".join(batch)]
KeyError: 'U_U_A_0_5_2_9_4_._1'
@HobnobMancer HobnobMancer linked a pull request Jun 16, 2024 that will close this issue
@HobnobMancer
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I am still working on this. I hope have working code on the issues-129-ncbi branch but next Monday 🤞

@HobnobMancer HobnobMancer self-assigned this Jul 1, 2024
@HobnobMancer HobnobMancer added bug Something isn't working enhancement New feature or request labels Jul 1, 2024
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