Database should be an amino acid fasta file with entry id's that can be parsed to obtain contig or scaffold ids referenced in your gff file

A ProtXML file produced by Protein Prophet

A gff3 file with coordinates for all protein entries used for proteomics searches. Coordinates should correspond to entries in the genome fasta file

Only peptides within accepted proteins and passing this threshold will appear in the output

Only peptides within proteins passing this threshold will appear in the output

Regex with capture group for parsing gff ids from protein ids

Regex with capture group for parsing genomic ids from protein ids

Regex to match protein ids that we should ignore completely