I have a set of SNPs for an organism for which annotation is still in progress. I obtained set of SNPs of interest and to get functional information I have GFF file with genes predicted by Augustus and GFF3 file with proteins annotation from InterProScan. Is there any tool that would let me integrate this information or will I be forced to write my own script? I didn't manage to find what I need so far but maybe I'm missing something.
So far I annotated my SNPs with augustus GFF file using snpEff but I can't do the same with InterProScan GFF3 file as I am having more or less this kind of output of building database for my organism:
Reading GFF3 data file : 'path_to_file' Total: 0 markers added.
Create exons from CDS (if needed): Exons created for 0 transcripts. Deleting redundant exons (if needed): Total transcripts with deleted exons: 0 Collapsing zero length introns (if needed): Total collapsed transcripts: 0 Reading sequences : Reading FASTA file: 'path_to_reference' Reading sequence 'scf_1', length: 2205567 Adding genomic sequences to exons: Done (0 sequences added, 0 ignored). Reading sequence 'scf_2', length: 1244474 Adding genomic sequences to exons: Done (0 sequences added, 0 ignored). Reading sequence 'scf_3', length: 1199189 Adding genomic sequences to exons: Done (0 sequences added, 0 ignored). Reading sequence 'scf_4', length: 3287760 Adding genomic sequences to exons: Done (0 sequences added, 0 ignored).
And later on:
Total: 0 sequences added, 0 sequences ignored. Adjusting transcripts: Adjusting genes: Adjusting chromosomes lengths: Ranking exons: Create UTRs from CDS (if needed): Correcting exons based on frame information. Remove empty chromosomes: Removing empty chromosome: 'g4789.t1' Removing empty chromosome: 'g7757.t1' Removing empty chromosome: 'g5919.t1'
It's the same for all scaffolds and genes - it looks to me like my genes are treated as chromosomes. How could I use this GFF3 file to biuld snpEff database for the annotation?