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gff-to-gtf off-by-one error? #7

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gedankenstuecke opened this issue Feb 20, 2017 · 0 comments
Open

gff-to-gtf off-by-one error? #7

gedankenstuecke opened this issue Feb 20, 2017 · 0 comments

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@gedankenstuecke
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I noticed some weird error when converting a GFF to GTF with gff_to_gtf.py.

This is the gene model in the original GFF:

scaffold_00034	JGI	exon	1	472	.	-	.	name "CLAGR_004651-RA"; transcriptId 5353
scaffold_00034	JGI	CDS	1	472	.	-	1	name "CLAGR_004651-RA"; proteinId 5305; exonNumber 3
scaffold_00034	JGI	exon	527	1274	.	-	.	name "CLAGR_004651-RA"; transcriptId 5353
scaffold_00034	JGI	CDS	527	1274	.	-	2	name "CLAGR_004651-RA"; proteinId 5305; exonNumber 2
scaffold_00034	JGI	exon	1326	1593	.	-	.	name "CLAGR_004651-RA"; transcriptId 5353
scaffold_00034	JGI	CDS	1326	1593	.	-	0	name "CLAGR_004651-RA"; proteinId 5305; exonNumber 1
scaffold_00034	JGI	start_codon	1591	1593	.	-	0	name "CLAGR_004651-RA"

The exon3 annotation goes from 1…472 on the - strand. After the conversion to GTF this is the result:

scaffold_00034	JGI	exon	0	472	.	-	.	gene_id "CLAGR_004651-RA"; transcript_id "5305"; exon_number "1"; gene_name "";
scaffold_00034	JGI	CDS	1	472	.	-	1	gene_id "CLAGR_004651-RA"; transcript_id "5305"; exon_number "1"; gene_name "";
scaffold_00034	JGI	start_codon	1591	1593	.	-	1	gene_id "CLAGR_004651-RA"; transcript_id "5305"; exon_number "1"; gene_name "";
scaffold_00034	JGI	exon	527	1274	.	-	.	gene_id "CLAGR_004651-RA"; transcript_id "5305"; exon_number "2"; gene_name "";
scaffold_00034	JGI	CDS	527	1274	.	-	2	gene_id "CLAGR_004651-RA"; transcript_id "5305"; exon_number "2"; gene_name "";
scaffold_00034	JGI	exon	1326	1593	.	-	.	gene_id "CLAGR_004651-RA"; transcript_id "5305"; exon_number "3"; gene_name "";
scaffold_00034	JGI	CDS	1326	1593	.	-	0	gene_id "CLAGR_004651-RA"; transcript_id "5305"; exon_number "3"; gene_name "";
scaffold_00034	JGI	stop_codon	1	3	.	-	0	gene_id "CLAGR_004651-RA"; transcript_id "5305"; exon_number "3"; gene_name "";

Somehow the exon now goes from 0…472 instead. I somehow assume it's a weird behavior if your feature borders to the end of the sequence?
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