Feature request: Parsing OrthoFinder output

[pnatsi]

Hi @fwhelan,

Just came across the biorXiv manuscript, impressive work! I am working on something similar, but using the OrthoFinder output instead of Roary.

Have you considered extending Coinfinder to accept OrthoFinder result as input? OrthoFinder is one of the most popular tools for homology inference across genomes.

Paschalis

[fwhelan]

Hi Paschalis,

Sure, this is something that I could consider doing. It shouldn't be too difficult to go from OrthoFinder's output to a tab delimited file of ortholog groups to genome IDs.

In the meantime, you could consider using coinfinder's -i option to input a tab-delimited list that you could make from your OrthoFinder results.

--Fiona

[ak-watson]

Sorry to revive an old feature request, just to add that I used the coinfinder -i option after parsing my OrthoFinder output to the tsv format and everything ran smoothly. It is pretty straight forward, but happy to tidy up my orthofinder2tsv script and share it if it is useful. I'll check how badly I hardcoded it...

[fwhelan]

Not at all!! I'm so glad to receive your comment!

If you are willing to share your script I would be more than happy to include it as part of this project! :)

[gao91]

The file from orthofinder is Orthogroups.tsv？

[CelinePetersen]

Hi @ak-watson, I would very much appreciate it if you could share your script. Hoping to hear from you!