public static RelationFile run(
String fasta, es.ehubio.proteomics.pipeline.Digester.Config digestion, int minPep, int maxPep)
throws IOException, InvalidSequenceException {
RelationFile relations = new RelationFile("protein", "peptideSequence");
for (Fasta protein : Fasta.readEntries(fasta, SequenceType.PROTEIN)) {
for (String pepSeq :
es.ehubio.proteomics.pipeline.Digester.digestSequence(protein.getSequence(), digestion)) {
if (pepSeq.length() < minPep || pepSeq.length() > maxPep) continue;
relations.addEntry(new Relation(protein.getAccession(), pepSeq));
}
}
return relations;
}
