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;
}
@Override
protected void run(List<Argument> args) throws Exception {
Enzyme enzyme = Enzyme.valueOf(getValue(Arguments.OPT_ENZYME));
int missedCleavages = getIntValue(Arguments.OPT_CLEAVAGES);
boolean usingDP = getBooleanValue(Arguments.OPT_ASP_PRO);
int cutNterm = getIntValue(Arguments.OPT_CUT_NTERM);
es.ehubio.proteomics.pipeline.Digester.Config digestion =
new es.ehubio.proteomics.pipeline.Digester.Config(
enzyme, missedCleavages, usingDP, cutNterm);
RelationFile relations =
run(
getValue(OPT_FASTA),
digestion,
getIntValue(Arguments.OPT_MIN_PEP_LEN),
getIntValue(Arguments.OPT_MAX_PEP_LEN));
relations.save(getValue(OPT_REL));
}