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@hotdogee hotdogee released this 01 Jul 18:08
· 4 commits to master since this release
2.3.0
efc495c

exonerate-gff3

This is an exonerate fork with added gff3 support.
Original website with user guides: http://www.ebi.ac.uk/~guy/exonerate/

New Option:
--gff3 [FALSE]

Using the "--gff3 yes" option with the "--showtargetgff yes" option will output GFF3. Without the "--gff3 yes" option, everything works just as before so previous scripts relying on the old output format won’t break.

Example Command:
exonerate.exe -q protein.fa -t genome.fa --model protein2genome --querytype protein --targettype dna --showvulgar no --softmaskquery yes --softmasktarget yes --minintron 20 --maxintron 3000 --showalignment no --showtargetgff yes --showcigar no --geneseed 250 --score 250 --verbose 0 --gff3 yes

Example Output:

Scaffold1   exonerate:protein2genome:local  match   188318  189587  649 -   .   ID=match00012;Name=EDAN000750-PA;Target=EDAN000750-PA 1 129 +;Gap=M135 D884 M251
Scaffold1   exonerate:protein2genome:local  match_part  189452  189587  .   -   .   Parent=match00012
Scaffold1   exonerate:protein2genome:local  match_part  188318  188568  .   -   .   Parent=match00012
Scaffold1   exonerate:protein2genome:local  match   183667  183897  392 -   .   ID=match00013;Name=EDAN000750-PA;Target=EDAN000750-PA 127 203;Gap=M231
Scaffold1   exonerate:protein2genome:local  match_part  183667  183897  .   -   .   Parent=match00013
Scaffold1   exonerate:protein2genome:local  match   45007   45165   265 -   .   ID=match00014;Name=EDAN000738-PA;Target=EDAN000738-PA 10 62;Gap=M159
Scaffold1   exonerate:protein2genome:local  match_part  45007   45165   .   -   .   Parent=match00014
Scaffold1   exonerate:protein2genome:local  match   218654  221996  1577    +   .   ID=match00015;Name=EDAN000753-PA;Target=EDAN000753-PA 1 337 +;Gap=M30 D61 M100 D61 M127 D373 M181 D56 M225 D1183 M189 D604 M153
Scaffold1   exonerate:protein2genome:local  match_part  218654  218685  .   +   .   Parent=match00015
Scaffold1   exonerate:protein2genome:local  match_part  218745  218846  .   +   .   Parent=match00015
Scaffold1   exonerate:protein2genome:local  match_part  218906  219034  .   +   .   Parent=match00015
Scaffold1   exonerate:protein2genome:local  match_part  219406  219586  .   +   .   Parent=match00015
Scaffold1   exonerate:protein2genome:local  match_part  219643  219867  .   +   .   Parent=match00015
Scaffold1   exonerate:protein2genome:local  match_part  221051  221239  .   +   .   Parent=match00015
Scaffold1   exonerate:protein2genome:local  match_part  221844  221996  .   +   .   Parent=match00015
Assets 3
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