I have a .gff3 file for an insect genome, which looks like the following:
> Scaffold1 I5K gene 30267 30861 . + . ID=OFAS000001;Name=OfasTmpM000001; > Scaffold1 I5K mRNA 30267 30861 . + . ID=OFAS000001-RA;Name=OfasTmpM000001-RA;Parent=OFAS000001; > Scaffold1 I5K exon 30267 30428 . + . ID=OFAS000001-RA-EXON01;Parent=OFAS000001-RA; > Scaffold1 I5K exon 30763 30861 . + . ID=OFAS000001-RA-EXON02;Parent=OFAS000001-RA; > Scaffold1 I5K CDS 30267 30428 . + 0 ID=OFAS000001-RA-CDS01;Parent=OFAS000001-RA; > Scaffold1 I5K CDS 30763 30861 . + 0 ID=OFAS000001-RA-CDS02;Parent=OFAS000001-RA; > Scaffold1 I5K gene 401906 407738 . + . ID=OFAS000002;Name=OfasTmpA000002; > Scaffold1 I5K mRNA 401906 407738 . + . ID=OFAS000002-RA;Name=OfasTmpA000002-RA;Parent=OFAS000002;Dbxref=Coils:Coil; > Scaffold1 I5K exon 401906 401926 . + . ID=OFAS000002-RA-EXON01;Parent=OFAS000002-RA; > Scaffold1 I5K exon 402939 407738 . + . ID=OFAS000002-RA-EXON02;Parent=OFAS000002-RA;
I have the corresponding genome and CDS fasta files. What I need from all of this is the sequence of each exon in one fasta file. I only want individual exons, nothing else. I've seen this: Extract Cds Fastas From A Gff Annotation + Reference Sequence which seeks to extract CDS sequences only, but I have no clue how to adapt this for my purpose (I'm not skilled in scripting). I've also searched for some scripts for my purpose, but everything I've seen deals with obtaining CDS sequences from .gff files. Any help would be most appreciated.