Modify the gff export from Apollo, changing Name to ID and to add UTR features.
For instance, the following export will be modified to:
SM_V7_ZW iris gene 52309880 52312410 . - . owner=XXX;ID=38776c44-0fa6-4d5e-a3c0-4d5d3a359faf;date_last_modified=2018-01-23;Name=Smp_336850;date_creation=2018-01-23
SM_V7_ZW iris mRNA 52309880 52312410 . - . owner=XXX;Parent=38776c44-0fa6-4d5e-a3c0-4d5d3a359faf;ID=ea036c7f-a83e-4873-aef5-bccca601ef9c;date_last_modified=2018-01-23;Name=Smp_336850.1;date_creation=2018-01-23
SM_V7_ZW iris CDS 52311450 52311467 . - 0 Parent=ea036c7f-a83e-4873-aef5-bccca601ef9c;ID=ea036c7f-a83e-4873-aef5-bccca601ef9c-CDS;Name=ea036c7f-a83e-4873-aef5-bccca601ef9c-CDS
SM_V7_ZW iris CDS 52309880 52310784 . - 0 Parent=ea036c7f-a83e-4873-aef5-bccca601ef9c;ID=ea036c7f-a83e-4873-aef5-bccca601ef9c-CDS;Name=ea036c7f-a83e-4873-aef5-bccca601ef9c-CDS
SM_V7_ZW iris exon 52311450 52312410 . - . Parent=ea036c7f-a83e-4873-aef5-bccca601ef9c;ID=d4c7fca8-6407-402c-a230-647a10aa24b4;Name=d4c7fca8-6407-402c-a230-647a10aa24b4
SM_V7_ZW iris exon 52309880 52310784 . - . Parent=ea036c7f-a83e-4873-aef5-bccca601ef9c;ID=61148130-f429-443e-bbda-6a8dc1d3549a;Name=61148130-f429-443e-bbda-6a8dc1d3549a
Which looks more tranditional output from gene predictor (e.g., Augustus), and UTRs were annotated:
SM_V7_ZW Apollo gene 52309880 52312410 . - . ID=Smp_336850
SM_V7_ZW Apollo mRNA 52309880 52312410 . - . ID=Smp_336850.1;Parent=Smp_336850
SM_V7_ZW Apollo CDS 52311450 52311467 . - 0 ID=Smp_336850.1.cds;Parent=Smp_336850.1
SM_V7_ZW Apollo CDS 52309880 52310784 . - 0 ID=Smp_336850.1.cds;Parent=Smp_336850.1
SM_V7_ZW Apollo exon 52311450 52312410 . - . Parent=Smp_336850.1
SM_V7_ZW Apollo exon 52309880 52310784 . - . Parent=Smp_336850.1
SM_V7_ZW Apollo five_prime_UTR 52311468 52312410 . - . Parent=Smp_336850.1
./convertApollo.sh
Will take the input gff (input.gff) and transform to output.gff