biocommons.seqrepo
biocommons.seqrepo copied to clipboard
Fail to fetch-load RefSeq sequences
Describe the bug Currently there's a bug in fetch-load method.
To Reproduce Steps to reproduce the behavior:
- Install seqrepo
- sudo mkdir -p /usr/local/share/seqrepo
- sudo chown $USER /usr/local/share/seqrepo
- seqrepo init -i some-name
- seqrepo fetch-load -i some-name -n RefSeq NC_000001.10 NC_000002.11
- See the error (below)
Traceback (most recent call last):
File "/Users/gromdimon/.local/share/virtualenvs/auto-acmg-zfFpTw_m/bin/seqrepo", line 8, in <module>
sys.exit(main())
^^^^^^
File "/Users/gromdimon/.local/share/virtualenvs/auto-acmg-zfFpTw_m/lib/python3.12/site-packages/biocommons/seqrepo/cli.py", line 732, in main
opts.func(opts)
File "/Users/gromdimon/.local/share/virtualenvs/auto-acmg-zfFpTw_m/lib/python3.12/site-packages/biocommons/seqrepo/cli.py", line 466, in fetch_load
if aliases_cur.fetchone() is not None:
^^^^^^^^^^^^^^^^^^^^
AttributeError: 'generator' object has no attribute 'fetchone'
Expected behavior Fetch-load should work properly.
Additional context This fixes the problem:
sed -i -e 's/if aliases_cur.fetchone() is not None/if next(aliases_cur, None) is not None/' \
<your-path-to-lib>/biocommons/seqrepo/cli.py