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NBISweden / AGAT

Another Gtf/Gff Analysis Toolkit
GNU General Public License v3.0
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add script to create ENA compliant file by adding info to CDS, specif… #412

Closed LucileSol closed 10 months ago

LucileSol commented 10 months ago

We needed a quick and dirty (and it is dirty) script to copy the attributes info from mRNA to CDS to make ENA compliant file, without changing the IDs or rerunning the all manage functional annotation script (specific for functionally annotated maker input).

MartinPippel commented 10 months ago

so for braker annotations that went into NBIS functional annotation pipeline, only a very tiny change needs to be done:

line 87: $desc2 =~/ID=(\S+);Parent=\S+;(Dbxref=\S+;)_AED=\S+;makerName=\S+;(.*)/; #;Parent=*;(*)maker_name=*;(*)/; needs to be adapted to: $desc2 =~/ID=(\S+);Parent=\S+;(Dbxref=\S+;)makerName=\S+;(.*)/; #;Parent=*;(*)maker_name=*;(*)/;

so we might just add a braker and maker argument to that script, (as well as some sanity checks) ?

Juke34 commented 10 months ago

Unfortunatly this script does not follow AGAT's requirements to be compatible with parameter file and other peculiarities. Any reason why you want to add that into AGAT? I guess the best would be to put it into GAAS repository (https://github.com/NBISweden/GAAS) which collect various kind of scripts.

LucileSol commented 10 months ago

@MartinPippel I agree just an argument is better @Juke34 we can add it to GAAS sure, I wanted to add it AGAT because it is gff related.

Juke34 commented 10 months ago

I can prepare a script more generalized that can be AGAT compatible see #413