BioPhi failed with HMMscanError: b'Parse failed (sequence file /var/folders/j7/j8sdcdk16nn_ngnyt1nc9vlw0000gn/T/tmpuhcuvvsc.fasta):\nLine 3: illegal character }\n\n' 0it [00:00, ?it/s]
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- Dominant language
- Python
- Stars
- 265
- Forks
- 65
- PR merge metrics
- No merged PRs in 30d
Description
I'm getting the following error when running BioPhi from the command line.
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First steps
- Read the whole issue, then the project's contributing guide.
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- Open a pull request that references the issue number.
Research direction
Reproduce the BioPhi command-line failure and inspect the temporary FASTA file referenced in the HMMscanError, especially line 3. Trace the command-line path that creates or passes this sequence file to HMMscan, then establish the expected behavior for the illegal character and verify it with a regression case.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100