GAG discards UTR features

[marchoeppner]

I am not sure this behaviour is by design, but GAG currently ejects UTR features into the file genome.ignored.gff , resulting in the final annotation genome.gff to have no UTR annotations either. This concerns features with the feature type:

five_prime_UTR
three_prime_UTR

However, these two features are perfectly valid within the GFF3 standar and probably shouldn't be ignored (?).

More information at: http://www.sequenceontology.org/gff3.shtml

[bruab]

@marchoeppner This is by design, or by laziness perhaps. Since UTR isn't included in the NCBI's .tbl file, we choose to ignore them. Including them in the output is non-trivial, since certain filters and fixes within GAG can shift the boundaries between CDS and UTR. It's doable, it's just more complicated than Read-Them-In-And-Write-Them-Out.

As long as this omission doesn't cause anybody trouble with their genome submission, fixing it is low-priority. If anyone gets errors or other flak due to the absence of UTR, we'll move it up the queue.

[marchoeppner]

Understood - maybe something for the future? We are using Gag and Annie for things other than NCBI tbl dumping, so not being able to parse all features makes things a little tricky. That being said, it is already a very useful tool as is!

[bruab]

We have decided to do this. Maybe next week, depending on how horribly some transcriptome submissions go ...

[bruab]

We will create new UTR features from scratch, rather than preserve the original ones. This is simpler, gets around the issue of fixes and filters shifting UTR boundaries.

[PaTapiaBioinfo]

I am not sure this behaviour is by design, but GAG currently ejects UTR features into the file genome.ignored.gff , resulting in the final annotation genome.gff to have no UTR annotations either. This concerns features with the feature type:

five_prime_UTR
three_prime_UTR

However, these two features are perfectly valid within the GFF3 standar and probably shouldn't be ignored (?).

More information at: http://www.sequenceontology.org/gff3.shtml

i solved it replacing the line 246 in src/gff_reader.py:

        elif ltype == 'start_codon' or ltype == 'stop_codon' or ltype == 'five_prime_UTR' or ltype == 'three_prime_UTR'

this mantain the UTR in the .gff output but i thinks that not valid for NCBI tbl