INCATools / INCATools/ontology-access-kit

similarity compare fails on CLI using `-set1-file` & `-set2-file` args with complaint about missing `@`

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Dominant language
Python
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198
Forks
35
Avg merge
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Merged PRs (30d)
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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

Open the contributing 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

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