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nathanweeks / exonerate

A fork of exonerate: a generic tool for sequence alignment
GNU General Public License v3.0
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exon don't show phase #20

Open shiyi-pan opened 3 years ago

shiyi-pan commented 3 years ago

Hi, I want to use exonerate to predict gene. but the result don't show the exon phase and result premature termination of the gene.here is my code

exonerate -t genome.fa -q query.fa --model protein2genome --bestn 1 --showtargetgff > exonerate.txt

and here is my partal result:

GWHACEC00000010 exonerate:protein2genome:local gene 47782722 47802710 5777 + . ID=0;Name=0;Alias=_E1;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local CDS 47782722 47782829 . + . ID=.;Name=.;Alias=.;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local exon 47782722 47782829 . + . ID=0;Name=0;Alias=_E1;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local splice5 47782830 47782831 . + . ID=1;Name=1;Alias=_E1;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local intron 47782830 47785356 . + . ID=1;Name=1;Alias=_E1;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local splice3 47785355 47785356 . + . ID=0;Name=0;Alias=_E1;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local CDS 47785357 47785428 . + . ID=.;Name=.;Alias=.;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local exon 47785357 47785428 . + . ID=0;Name=0;Alias=_E1;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local splice5 47785429 47785430 . + . ID=2;Name=2;Alias=_E1;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local intron 47785429 47785584 . + . ID=2;Name=2;Alias=_E1;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local splice3 47785583 47785584 . + . ID=1;Name=1;Alias=_E1;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local CDS 47785585 47785639 . + . ID=.;Name=.;Alias=.;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local exon 47785585 47785639 . + . ID=0;Name=0;Alias=_E1;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local splice5 47785640 47785641 . + . ID=3;Name=3;Alias=_E1;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local intron 47785640 47785759 . + . ID=3;Name=3;Alias=_E1;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local splice3 47785758 47785759 . + . ID=2;Name=2;Alias=_E1;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local CDS 47785760 47785902 . + . ID=.;Name=.;Alias=.;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local exon 47785760 47785902 . + . ID=0;Name=0;Alias=_E1;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local splice5 47785903 47785904 . + . ID=4;Name=4;Alias=_E1;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local intron 47785903 47786085 . + . ID=4;Name=4;Alias=_E1;Parent=0;Target=. GWHACEC00000010 exonerate:protein2genome:local splice3 47786084 47786085 . + . ID=3;Name=3;Alias=_E1;Parent=0;Target=.

could you tell how to add phase information at the eighth column , thank you very much.