agat_sp_flag_short_introns.pl not flagging a 1 bp intron

[GallVp]

Thank you once again for the excellent tool and fast response to issues.

Describe the bug
agat_sp_flag_short_introns.pl seem to be not flagging a 1 bp intron in the attached GFF file. Although, it is flagging another 66 bp intron in the next gene. I am not sure what's happening.

General (please complete the following information):

• AGAT version: quay.io/biocontainers/agat:1.4.1--pl5321hdfd78af_0
• OS: macOS

To Reproduce

agat_sp_flag_short_introns.pl -g test.gff -i 100 -o flagged.output.gff

Expected behavior

Both genes should be flagged with pseudo= attribute. But only the second gene gene28774 is flagged.

test.gff

##gff-version 3
scaffold_4	AGAT	gene	8631766	8635584	.	+	.	ID=gene28773;description=Hypothetical protein | no eggnog hit
scaffold_4	Liftoff	mRNA	8631766	8635584	.	+	.	ID=gene28773.t1;Parent=gene28773;description=Hypothetical protein | no eggnog hit
scaffold_4	Liftoff	exon	8631766	8634966	.	+	.	ID=gene28773.t1.exon1;Parent=gene28773.t1
scaffold_4	Liftoff	exon	8634968	8635584	.	+	.	ID=gene28773.t1.exon2;Parent=gene28773.t1
scaffold_4	Liftoff	CDS	8632667	8632951	.	+	0	ID=gene28773.t1.cds1;Parent=gene28773.t1
scaffold_4	AGAT	five_prime_UTR	8631766	8632666	.	+	.	ID=agat-five_prime_utr-1269;Parent=gene28773.t1
scaffold_4	Liftoff	intron	8634967	8634967	.	+	.	ID=intron_added-90678;Parent=gene28773.t1
scaffold_4	AGAT	three_prime_UTR	8632952	8634966	.	+	.	ID=agat-three_prime_utr-854;Parent=gene28773.t1
scaffold_4	AGAT	three_prime_UTR	8634968	8635584	.	+	.	ID=agat-three_prime_utr-855;Parent=gene28773.t1
scaffold_4	AUGUSTUS	gene	8720203	8721055	.	-	.	ID=gene28774;description=F-box kelch-repeat protein
scaffold_4	AUGUSTUS	mRNA	8720203	8721055	0.53	-	.	ID=gene28774.t1;Parent=gene28774;description=F-box kelch-repeat protein
scaffold_4	AUGUSTUS	exon	8720203	8720819	.	-	.	ID=gene28774.t1.exon1;Parent=gene28774.t1
scaffold_4	AUGUSTUS	exon	8720887	8721055	.	-	.	ID=gene28774.t1.exon2;Parent=gene28774.t1
scaffold_4	AUGUSTUS	CDS	8720203	8720819	.	-	2	ID=gene28774.t1.cds1;Parent=gene28774.t1
scaffold_4	AUGUSTUS	CDS	8720887	8721055	.	-	0	ID=gene28774.t1.cds2;Parent=gene28774.t1
scaffold_4	AUGUSTUS	intron	8720820	8720886	.	-	.	ID=intron_added-90679;Parent=gene28774.t1

[Juke34]

Hi,

Right the script focus on short intron in CDS (If I remember well it is because it was the only case problematic when submitting to INSDC). This is a mistake to not have include this information in the doc.
But we can definitely update the script to flag all short introns.

[GallVp]

Hi @Juke34

Thank you. I would be great to have the ability to flag all the short introns.

[Juke34]

I renamed the previous script into agat_sp_flag_short_introns_ebi.pl
It was too specific. The flag was specific to EBI to pass the submission process.
attributes was also modified into attributes when flagged to pass the EBI specification.

So I created a new agat_sp_flag_short_introns.pl that looks at the exon (from coding or non coding gene) and flagging with the <short_intron> attribute and that it. Could you give a try? It is in the branch 516

[GallVp]

Thank you!

I have tested both agat_sp_flag_short_introns.pl and agat_sp_flag_short_introns_ebi.pl. They seem to be on the example GFF pasted in the issue body.

[Juke34]

fixed and merged in #518