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NBISweden / AGAT

Another Gtf/Gff Analysis Toolkit
GNU General Public License v3.0
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annotation remark feature #18

Closed mictadlo closed 4 years ago

mictadlo commented 4 years ago

Hi, I used agat_sp_complement_annotations.pl and it created the following GFF3 file:

##gff-version 3
##sequence-region NbV1Ch01 1 187295484
NbV1Ch01        annotation      remark  1       187295484       .       .       .       gff-version=3;sequence-region=%28%27NbV1Ch01%27%2C 0%2C 187295484%29
NbV1Ch01        transdecoder    gene    98185   99705   .       -       .       ID=NBlab01G00010
NbV1Ch01        transdecoder    mRNA    98185   99705   .       -       .       ID=NBlab01G00010.1;Parent=NBlab01G00010
NbV1Ch01        transdecoder    exon    98185   98571   .       -       .       ID=NBlab01G00010.1.exon4;Parent=NBlab01G00010.1
NbV1Ch01        transdecoder    exon    98679   98844   .       -       .       ID=NBlab01G00010.1.exon3;Parent=NBlab01G00010.1
NbV1Ch01        transdecoder    exon    99134   99325   .       -       .       ID=NBlab01G00010.1.exon2;Parent=NBlab01G00010.1
NbV1Ch01        transdecoder    exon    99417   99705   .       -       .       ID=NBlab01G00010.1.exon1;Parent=NBlab01G00010.1
NbV1Ch01        transdecoder    CDS     98186   98571   .       -       2       ID=NBlab01G00010.1.cds;Parent=NBlab01G00010.1
NbV1Ch01        transdecoder    CDS     98679   98844   .       -       0       ID=NBlab01G00010.1.cds;Parent=NBlab01G00010.1
NbV1Ch01        transdecoder    CDS     99134   99325   .       -       0       ID=NBlab01G00010.1.cds;Parent=NBlab01G00010.1
NbV1Ch01        transdecoder    CDS     99417   99704   .       -       0       ID=NBlab01G00010.1.cds;Parent=NBlab01G00010.1
NbV1Ch01        transdecoder    five_prime_UTR  99705   99705   .       -       .       ID=NBlab01G00010.1.5UTRg1;Parent=NBlab01G00010.1
NbV1Ch01        transdecoder    three_prime_UTR 98185   98185   .       -       .       ID=NBlab01G00010.1.3UTRg1;Parent=NBlab01G00010.1

However looking at the GFF3 specifications they do not have annotation remark feature.

Is there a way to disableannotation remark in agat_sp_complement_annotations.pl?

Thank you in advance,

Michal

Juke34 commented 4 years ago

I'm not sure to understand how you get this line 

NbV1Ch01        annotation      remark  1       187295484       .       .       .       gff-version=3;sequence-region=%28%27NbV1Ch01%27%2C 0%2C 187295484%29

Is it a copy past problem here?

remark feature should be trowed away as long you have not specified to keep it in the features_level1.json parameter file.

I have done a check locally and don't get the result you describe.

mictadlo commented 4 years ago

I am sorry, it was added accidentally by one of the scripts.