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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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