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NBISweden / AGAT

Another Gtf/Gff Analysis Toolkit
GNU General Public License v3.0
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Exonerate gff conversion error with AGAT #350

Closed davidcoolman closed 1 year ago

davidcoolman commented 1 year ago

Sample file with problem in standardizing

ptg000001l  exonerate:protein2genome:local  gene    13733550    13734381    1150    -   .   gene_id 1 ; sequence XP_021634939.1 ; gene_orientation +
ptg000001l  exonerate:protein2genome:local  cds 13734028    13734381    .   -   .
ptg000001l  exonerate:protein2genome:local  exon    13734028    13734381    .   -   .   insertions 0 ; deletions 0
ptg000001l  exonerate:protein2genome:local  splice5 13734026    13734027    .   -   .   intron_id 1 ; splice_site "GT"
ptg000001l  exonerate:protein2genome:local  intron  13733971    13734027    .   -   .   intron_id 1
ptg000001l  exonerate:protein2genome:local  splice3 13733971    13733972    .   -   .   intron_id 0 ; splice_site "AG"
ptg000001l  exonerate:protein2genome:local  cds 13733550    13733970    .   -   .
ptg000001l  exonerate:protein2genome:local  exon    13733550    13733970    .   -   .   insertions 0 ; deletions 0 ; frameshifts 1
ptg000001l  exonerate:protein2genome:local  gene    6876023 6876853 1131    -   .   gene_id 2 ; sequence XP_021634939.1 ; gene_orientation +
ptg000001l  exonerate:protein2genome:local  cds 6876500 6876853 .   -   .
ptg000001l  exonerate:protein2genome:local  exon    6876500 6876853 .   -   .   insertions 0 ; deletions 0
ptg000001l  exonerate:protein2genome:local  splice5 6876498 6876499 .   -   .   intron_id 1 ; splice_site "GT"
ptg000001l  exonerate:protein2genome:local  intron  6876443 6876499 .   -   .   intron_id 1
ptg000001l  exonerate:protein2genome:local  splice3 6876443 6876444 .   -   .   intron_id 0 ; splice_site "AG"
ptg000001l  exonerate:protein2genome:local  cds 6876023 6876442 .   -   .
ptg000001l  exonerate:protein2genome:local  exon    6876023 6876442 .   -   .   insertions 0 ; deletions 0

Add splice5 and splice3 as features.