INCATools / INCATools/ontology-access-kit
similarity compare fails on CLI using `-set1-file` & `-set2-file` args with complaint about missing `@`
- Dominant language
- Python
- Stars
- 198
- Forks
- 35
- Avg merge
- 3d 4h
- Merged PRs (30d)
- 1
Description
I'm running
```
runoak -i phenio.db similarity -p i –set1-file my_mp_terms.txt –set2-file all_hp_terms.txt -O csv
```
and it's failing with `ValueError: '@' is not in list`
It's working successfully with:
```
runoak -i semsimian:../../semsimian-server/phenio.db similarity -p i .idfile high_confidence_phenotyptes.tsv @ .idfile all_hp.tsv -O tsv
```
(apparently just a small CLI bug)
Contributor guide
Research direction
Start with the similarity CLI argument parsing for `-set1-file` and `-set2-file`, comparing it with the working positional syntax that includes `@`. Reproduce the reported command and confirm it completes without the `ValueError: '@' is not in list` error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 55/100