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IndexError: list index out of range #1

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cwb14 opened this issue Sep 15, 2022 · 0 comments
Open

IndexError: list index out of range #1

cwb14 opened this issue Sep 15, 2022 · 0 comments

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@cwb14
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cwb14 commented Sep 15, 2022

Hi,

I am trying to run makePAV.py and bumping into an issue. I suspect that my inputs are not formatted correctly. I am running python makePAV.py ExonsOnly.gff2bed.bed All.per_base.exons.bed > test.tsv. My inputs are ExonsOnly.gff2bed.bed, which looks like:

1A_a	36329	36387	.	.	-	AUGUSTUS	exon	.	ID=ajg16045.t1.exon1;Parent=ajg16045.t1;
1A_a	36329	36387	.	.	-	AUGUSTUS	exon	.	ID=ajg16045.t2.exon1;Parent=ajg16045.t2;
1A_a	36475	36570	.	.	-	AUGUSTUS	exon	.	ID=ajg16045.t1.exon2;Parent=ajg16045.t1;
1A_a	36475	36570	.	.	-	AUGUSTUS	exon	.	ID=ajg16045.t2.exon2;Parent=ajg16045.t2;
1A_a	37442	37491	.	.	-	AUGUSTUS	exon	.	ID=ajg16045.t2.exon3;Parent=ajg16045.t2;

and All.per_base.exons.bed, which looks like:

1A_a	35	112	2
1A_a	112	113	3
1A_a	113	132	4
1A_a	132	133	3
1A_a	133	142	5

Any advice is appreciated. Thank you.

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