Extra script: annotate Orthogroups (HOG) from fasta descriptions #434
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
ViriatoII
changed the title
|
Cool! I updated my script accordingly. https://binfgitlab.unibe.ch/troder/orthofinder_tools/-/commit/1262643b53ed7f163f8017407fd0d6f777a5b946 |
MrTomRod
pushed a commit
to MrTomRod/orthofinder-tools
that referenced
this pull request
Mar 21, 2022
…l/434) - compatible with new N0.tsv structure - small tweek to ignore proteins annotated AbInitio with maker, which don't have useful information, and to be resilient to gene names missing in the corresponding fastas
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Hi
I edited the script of @MrTomRod to be applicable to the new N0.tsv structure of Orthofinder. I also made a small tweek to ignore proteins annotated AbInitio with maker, which don't have useful information, and to be resilient to gene names missing in the corresponding fastas.
Asked for in:
#362
#373
Massive thanks to @MrTomRod
The script is here: annotate_N0.txt (.txt due to github requirements, I've never done a pull request before)
EDIT: Oh, I notice now that you wanted to remove dependencies. Sorry, I didn't do that!
Cheers,
Ricardo