sokrypton / sokrypton/ColabFold
Unnecessary calculation of MSA?
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Description
In the recent fix to search for templates when a3m MSA is present:
https://github.com/sokrypton/ColabFold/blob/10b425d76c743eb3ece8b3dc68e117d0b2a89a16/colabfold/batch.py#L1336
isn't the get_msa_and_templates calculating a3m MSA on the remote server anyway? This seems unnecessary and should instead send the local a3m to the server.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start in colabfold/batch.py around line 1336 and inspect get_msa_and_templates, along with the referenced commit. Trace whether an existing local a3m MSA is recalculated remotely; done means the local a3m is sent to the server instead, with the unnecessary calculation avoided.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Refactor
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100