INCATools / INCATools/ontology-access-kit
Reproducing the enrichment example from today's OBO tutorial
- Dominant language
- Python
- Stars
- 198
- Forks
- 35
- Avg merge
- 3d 4h
- Merged PRs (30d)
- 1
Description
cc: @cmungall @matentzn
From this slide:
https://docs.google.com/presentation/d/1b714y5W9EdjypwrHKNdDT4liVqMIbsIDfGxxrVWFxc0/edit#slide=id.g215fddbc4d6_0_181
My understanding is that the code should be:
```bash
runoak -i sqlite:obo:mondo normalize -M OMIM .desc//p=i EDS | grep -v ^id > omim.txt
runoak -i sqlite:obo:hp enrichment -p i -U omim.txt
```
> PS: There is a typo in the presentation I think, the '-M' is not in capital
This gives me the following error when running `enrichment`:
```
AttributeError: 'NoneType' object has no attribute 'lookup'
```
My `omim.txt` file looks like this, not sure it's the right format:
```
OMIM:130020 None
OMIM:130050 None
OMIM:130060 None
OMIM:130090 None
OMIM:147900 None
OMIM:225310 None
OMIM:225320 None
OMIM:225410 None
OMIM:305200 None
OMIM:606408 None
OMIM:608763 None
OMIM:612350 None
OMIM:614170 None
OMIM:614557 None
OMIM:615349 None
OMIM:615539 None
OMIM:617174 None
OMIM:225400 None
OMIM:130000 None
OMIM:130010 None
OMIM:601776 None
OMIM:130070 None
OMIM:130080 None
OMIM:229200 None
OMIM:619115 None
OMIM:619120 None
OMIM:616471 None
OMIM:617821 None
OMIM:618000 None
```
Contributor guide
Research direction
Start by running the two `runoak` commands from the issue and inspect the reported `NoneType` lookup failure in the `enrichment` entry point. Compare the generated `omim.txt` contents with the tutorial example; done means the commands run successfully with the expected input format.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100