sequaljs/dist/__test__/proforma.test.js

JavaScript/TypeScript library for parsing and manipulating ProForma peptide sequence notation

"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
// src/__tests__/proforma.test.ts
const proforma_1 = require("../proforma");
describe('ProFormaParser', () => {
    describe('Basic sequence parsing', () => {
        it('should parse a simple peptide sequence', () => {
            const input = 'PEPTIDE';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            expect(Object.keys(mods).length).toBe(0);
            expect(globalMods.length).toBe(0);
            expect(ambiguities.length).toBe(0);
        });
    });
    describe('Terminal modifications', () => {
        it('should parse N-terminal modification', () => {
            const input = '[Acetyl]-PEPTIDE';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            expect(mods[-1].length).toBe(1);
            expect(mods[-1][0].modValue.primaryValue).toBe('Acetyl');
            expect(mods[-1][0].modType).toBe('terminal');
        });
        it('should parse C-terminal modification', () => {
            const input = 'PEPTIDE-[Amidated]';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            expect(mods[-2].length).toBe(1);
            expect(mods[-2][0].modValue.primaryValue).toBe('Amidated');
            expect(mods[-2][0].modType).toBe('terminal');
        });
        it('should parse both terminal modifications', () => {
            const input = '[Acetyl]-PEPTIDE-[Amidated]';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            expect(mods[-1].length).toBe(1);
            expect(mods[-2].length).toBe(1);
        });
    });
    describe('Global modifications', () => {
        it('should parse fixed modifications', () => {
            const input = '<Carbamidomethyl@C>PEPCTIDE';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPCTIDE');
            expect(globalMods.length).toBe(1);
            expect(globalMods[0].modValue.primaryValue).toBe('Carbamidomethyl');
            expect(globalMods[0].targetResidues).toEqual(['C']);
            expect(globalMods[0].modType).toBe('global');
            expect(globalMods[0].globalModType).toBe('fixed');
        });
        it('should parse isotope labeling', () => {
            const input = '<15N>PEPTIDE';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            expect(globalMods.length).toBe(1);
            expect(globalMods[0].modValue.primaryValue).toBe('15N');
            expect(globalMods[0].globalModType).toBe('isotope');
        });
        it('should parse multiple global modifications', () => {
            const input = '<Carbamidomethyl@C><15N>PEPCTIDE';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(globalMods.length).toBe(2);
        });
    });
    describe('Site-specific modifications', () => {
        it('should parse single modification', () => {
            const input = 'PEP[Phospho]TIDE';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            expect(mods[2].length).toBe(1);
            expect(mods[2][0].modValue.primaryValue).toBe('Phospho');
        });
        it('should parse multiple modifications', () => {
            const input = 'PE[Phospho]PT[Phospho]IDE';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            expect(mods['1'].length).toBe(1);
            expect(mods['3'].length).toBe(1);
        });
        it('should parse mass shift modifications', () => {
            const input = 'PEP[+79.966]TIDE';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            expect(mods[2].length).toBe(1);
            expect(mods[2][0].mass).toBeCloseTo(79.966);
        });
    });
    describe('Sequence ambiguities', () => {
        it('should parse sequence ambiguity notation', () => {
            const input = 'PEP(?AB)TIDE';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            expect(ambiguities.length).toBe(1);
            expect(ambiguities[0].value).toBe('AB');
            expect(ambiguities[0].position).toBe(0);
        });
    });
    describe('Labile modifications', () => {
        it('should parse labile modifications', () => {
            const input = '{Glycan:HexNAc}PEPTIDE';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            expect(mods[-3].length).toBe(1);
            expect(mods[-3][0].modValue.primaryValue).toBe('HexNAc');
            expect(mods[-3][0].modValue.pipeValues[0].isValidGlycan).toBe(true);
            expect(mods[-3][0].modType).toBe('labile');
        });
    });
    describe('Unknown position modifications', () => {
        it('should parse unknown position modifications', () => {
            const input = '[Phospho]?PEPTIDE';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            expect(mods[-4].length).toBe(1);
            expect(mods[-4][0].modValue.primaryValue).toBe('Phospho');
            expect(mods[-4][0].modType).toBe('unknown_position');
        });
        it('should parse multiple unknown position modifications', () => {
            const input = '[Phospho][Acetyl]?PEPTIDE';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            expect(mods[-4].length).toBe(2);
        });
    });
    describe('Range modifications', () => {
        it('should parse range modifications', () => {
            const input = 'PE(PTI)DE';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            // No modifications yet, just testing the range parsing
        });
        it('should parse range with modifications', () => {
            const input = 'PE(PTI)[Phospho]DE';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            expect(mods[2].length).toBe(1);
            expect(mods[3].length).toBe(1);
            expect(mods[4].length).toBe(1);
            expect(mods[2][0].inRange).toBe(true);
        });
    });
    describe('Crosslinks and branches', () => {
        it('should parse crosslinks', () => {
            const input = 'PEPTIDE[DSS#XL1]KLMN[#XL1]';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDEKLMN');
            expect(mods[6][0].crosslinkId).toBe('XL1');
            expect(mods[10][0].isCrosslinkRef).toBe(true);
        });
        it('should parse branch modifications', () => {
            const input = 'PEPTIDE[Glycan#BRANCH]K[#BRANCH]';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDEK');
            expect(mods[6][0].modValue.isBranch).toBe(true);
            expect(mods[7][0].modValue.isBranchRef).toBe(true);
        });
    });
    describe('Ambiguity groups', () => {
        it('should parse ambiguity groups', () => {
            const input = 'PEPT[Phospho#1]IDE[Phospho#1]';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            expect(mods[3][0].ambiguityGroup).toBe('1');
            expect(mods[6][0].ambiguityGroup).toBe('1');
        });
        it('should parse ambiguity groups with localization scores', () => {
            const input = 'PEPT[Phospho#1(0.8)]IDE[Phospho#1(0.2)]';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(mods[3][0].localizationScore).toBe(0.8);
            expect(mods[6][0].localizationScore).toBe(0.2);
        });
        it('should parse ambiguity reference', () => {
            const input = 'PEPT[Phospho#1]IDE[#1]';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(mods[3][0].ambiguityGroup).toBe('1');
            expect(mods[6][0].ambiguityGroup).toBe('1');
            expect(mods[6][0].isAmbiguityRef).toBe(true);
        });
    });
    describe('Complex examples', () => {
        it('should parse a complex ProForma string with multiple features', () => {
            const input = '<Carbamidomethyl@C>[Acetyl]-PEPC[+57.021]T[Phospho]IDE-[Amidated]';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPCTIDE');
            expect(globalMods.length).toBe(1);
            expect(mods[-1]).toBeDefined(); // N-term mod
            expect(mods[-2]).toBeDefined(); // C-term mod
            expect(mods[3]).toBeDefined(); // Cysteine mod
            expect(mods[4]).toBeDefined(); // Threonine phosphorylation
        });
    });
    describe('INFO tags support', () => {
        it('should parse basic INFO tags', () => {
            const input = 'ELVIS[Phospho|INFO:newly discovered]K';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('ELVISK');
            expect(mods[4].length).toBe(1);
            expect(mods[4][0].modValue.primaryValue).toBe('Phospho');
            expect(mods[4][0].modValue.infoTags.length).toBe(1);
            expect(mods[4][0].modValue.infoTags[0]).toBe('newly discovered');
        });
        it('should parse multiple INFO tags', () => {
            const input = 'ELVIS[Phospho|INFO:newly discovered|INFO:Created on 2021-06]K';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('ELVISK');
            expect(mods[4].length).toBe(1);
            expect(mods[4][0].modValue.primaryValue).toBe('Phospho');
            expect(mods[4][0].modValue.infoTags.length).toBe(2);
            expect(mods[4][0].modValue.infoTags[0]).toBe('newly discovered');
            expect(mods[4][0].modValue.infoTags[1]).toBe('Created on 2021-06');
        });
        it('should parse N-terminal modifications with INFO tags', () => {
            const input = '[Acetyl|INFO:Added during processing]-PEPTIDE';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            expect(mods[-1].length).toBe(1);
            expect(mods[-1][0].modValue.primaryValue).toBe('Acetyl');
            expect(mods[-1][0].modValue.infoTags.length).toBe(1);
            expect(mods[-1][0].modValue.infoTags[0]).toBe('Added during processing');
        });
        it('should parse C-terminal modifications with INFO tags', () => {
            const input = 'PEPTIDE-[Amidated|INFO:Common C-terminal mod]';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            expect(mods[-2].length).toBe(1);
            expect(mods[-2][0].modValue.primaryValue).toBe('Amidated');
            expect(mods[-2][0].modValue.infoTags.length).toBe(1);
            expect(mods[-2][0].modValue.infoTags[0]).toBe('Common C-terminal mod');
        });
        it('should parse global isotope modifications with INFO tags', () => {
            const input = '<13C|INFO:Stable isotope labeling>PEPTIDE';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            expect(globalMods.length).toBe(1);
            expect(globalMods[0].modValue.primaryValue).toBe('13C');
            expect(globalMods[0].globalModType).toBe('isotope');
            expect(globalMods[0].modValue.infoTags.length).toBe(1);
            expect(globalMods[0].modValue.infoTags[0]).toBe('Stable isotope labeling');
        });
        it('should parse global fixed modifications with INFO tags', () => {
            const input = '<[Carbamidomethyl|INFO:Standard alkylation]@C>PEPTCDE';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTCDE');
            expect(globalMods.length).toBe(1);
            expect(globalMods[0].modValue.primaryValue).toBe('Carbamidomethyl');
            expect(globalMods[0].globalModType).toBe('fixed');
            expect(globalMods[0].targetResidues).toEqual(['C']);
            expect(globalMods[0].modValue.infoTags.length).toBe(1);
            expect(globalMods[0].modValue.infoTags[0]).toBe('Standard alkylation');
        });
        it('should parse complex combinations with multiple INFO tags', () => {
            const input = '<[Carbamidomethyl|INFO:Standard alkylation]@C>[Acetyl|INFO:Added during processing]-PEPTC[+57.021|INFO:Mass verified]DE-[Amidated|INFO:Common C-terminal mod]';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTCDE');
            // Check global mod
            expect(globalMods.length).toBe(1);
            expect(globalMods[0].modValue.primaryValue).toBe('Carbamidomethyl');
            expect(globalMods[0].modValue.infoTags.length).toBe(1);
            expect(globalMods[0].modValue.infoTags[0]).toBe('Standard alkylation');
            // Check N-terminal mod
            expect(mods[-1].length).toBe(1);
            expect(mods[-1][0].modValue.primaryValue).toBe('Acetyl');
            expect(mods[-1][0].modValue.infoTags.length).toBe(1);
            expect(mods[-1][0].modValue.infoTags[0]).toBe('Added during processing');
            // Check C-terminal mod
            expect(mods[-2].length).toBe(1);
            expect(mods[-2][0].modValue.primaryValue).toBe('Amidated');
            expect(mods[-2][0].modValue.infoTags.length).toBe(1);
            expect(mods[-2][0].modValue.infoTags[0]).toBe('Common C-terminal mod');
            // Check residue mod
            expect(mods[4].length).toBe(1);
            expect(mods[4][0].mass).toBeCloseTo(57.021);
            expect(mods[4][0].modValue.infoTags.length).toBe(1);
            expect(mods[4][0].modValue.infoTags[0]).toBe('Mass verified');
        });
        it('should handle INFO tags with special characters', () => {
            const input = 'PEP[Phospho|INFO:MS/MS score=0.98|INFO:RT=34.5 min]TIDE';
            const [sequence, mods, globalMods, ambiguities] = proforma_1.ProFormaParser.parse(input);
            expect(sequence).toBe('PEPTIDE');
            expect(mods[2].length).toBe(1);
            expect(mods[2][0].modValue.primaryValue).toBe('Phospho');
            expect(mods[2][0].modValue.infoTags.length).toBe(2);
            expect(mods[2][0].modValue.infoTags[0]).toBe('MS/MS score=0.98');
            expect(mods[2][0].modValue.infoTags[1]).toBe('RT=34.5 min');
        });
    });
});