Semi-specific digestion in the IteratorFactory

[wenbostar]

Is there a way to do semi-tryptic digestion using the getSequenceIterator function from IteratorFactory?

[hbarsnes]

Yes, I think you should be able to do something like this:

DigestionParameters digestionPreferences = new DigestionParameters();
digestionPreferences.setCleavageParameter(DigestionParameters.CleavageParameter.enzyme);
digestionPreferences.addEnzyme(enzymeFactory.getEnzyme("Trypsin"));
SequenceIterator sequenceIterator = iteratorFactoryNoModifications.getSequenceIterator(yourSequence, digestionPreferences, 0.0, Double.MAX_VALUE);

[wenbostar]

Hi @hbarsnes , thanks. Which parameter in the code is used to control for semi-digestion?

[hbarsnes]

Ah, sorry, forgot to add the semi-specific part. See the fourth line below.

DigestionParameters digestionPreferences = new DigestionParameters();
digestionPreferences.setCleavageParameter(DigestionParameters.CleavageParameter.enzyme);
digestionPreferences.addEnzyme(enzymeFactory.getEnzyme("Trypsin"));
digestionPreferences.setSpecificity("Trypsin", Specificity.semiSpecific);
SequenceIterator sequenceIterator = iteratorFactoryNoModifications.getSequenceIterator(yourSequence, digestionPreferences, 0.0, Double.MAX_VALUE);

[wenbostar]

It looks like this doesn't work.

void testSemi_digestion(){
        IteratorFactory iteratorModifications = new IteratorFactory(new ArrayList<>());
        DigestionParameters digestionPreferences = new DigestionParameters();
        digestionPreferences.setCleavageParameter(DigestionParameters.CleavageParameter.enzyme);
        digestionPreferences.addEnzyme(EnzymeFactory.getInstance().getEnzyme("Trypsin"));
        digestionPreferences.setSpecificity("Trypsin", DigestionParameters.Specificity.semiSpecific);

        try {
            SequenceIterator sequenceIterator = iteratorModifications.getSequenceIterator("MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYR", digestionPreferences, 0.0, Double.MAX_VALUE);
            ExtendedPeptide extendedPeptide;
            while (true) {
                try {
                    if ((extendedPeptide = sequenceIterator.getNextPeptide()) == null) {
                        break;
                    }

                    Peptide peptide = extendedPeptide.peptide;
                    System.out.println(peptide.getSequence());

                } catch (InterruptedException e) {
                    e.printStackTrace();
                }



            }
        } catch (InterruptedException e) {
            throw new RuntimeException(e);
        }
    }

Output:

MTEYK
LVVVGAGGVGK
SALTIQLIQNHFVDEYDPTIEDSYR

Utilities version: 5.0.39.

[wenbostar]

Does this indicate semi-digestion is not implemented yet? https://github.com/compomics/compomics-utilities/blob/master/src/test/java/com/compomics/util/test/experiment/sequences/digestion/ProteinSequenceIteratorTest.java#L244

[hbarsnes]

Seems like you are correct in that the support for semi-specific has not been implemented for the IteratorFactory. I'll add it to the list of requested features, but I'm afraid that we will not have the resources to look into it at the moment.