Thomas Roder

It does! I forgot to document the recent changes I made to the script. Sorry. It should work now if you follow the manual: https://github.com/MrTomRod/orthofinder-tools/blob/master/README.md

Yes, you have to use the new N0 file. ``` OrthogroupToGeneName( n0_tsv='orthofinder_output/Phylogenetic_Hierarchical_Orthogroups/N0.tsv', index_column='HOG' ).run( fasta_dir=PATH_TO_ORTHOFINDER_FASTAS, file_endings='faa', out='path/to/output.tsv' ) ``` The annotations come from the fasta files. (`PATH_TO_ORTHOFINDER_FASTAS`)

> Ok cool, I just got it to run! So basically, we provide annotations as the description? for each gene that was assigned to an orthgroup, the script takes the...

You can't find the folder `Phylogenetic_Hierarchical_Orthogroups`? Are you using the latest version of Orthofinder? Because older versions don't create it. Here are the [instructions](https://github.com/MrTomRod/orthofinder-tools/blob/master/README.md) for my script.

Please show me the first 5 lines of one of your fasta files.

no, the first 5 lines of one of your **FASTA** files.

The reason is that your fastas are not functionally annotated. My script only works if your fastas look something like this: ``` >L022000001-T1 L022_000001 Description Gene 1 MFCPMDPPVEDSVVRTGENRWSLGSLYVCELVYDVPNDAMASWEADGNTYCIRKSSKDEQPSTVLGDSGSNRIHHAGTS >L022000001-T1 L022_000001...

> Any such luck for Proteomes downloaded from uniprot? This is an example header: ``` >tr|A0A151G869|A0A151G869_LACPN Bacteriocin immunity protein OS=Lactiplantibacillus plantarum OX=1590 GN=AYO51_00560 PE=4 SV=1 ``` If you change these...

I don't think the existing API enables me to do what I want, i.e., to remove only _certain_ hyperlinks, namely those that start with `https://sciwheel.com/`. Thanks for the `clone_from` hint,...

Yes, I already managed to do what I wanted. The point is that my solution is more flexible and would imo improve your library. Feel free to close this issue...