Protein

class

 new Protein() 

class Protein {

    constructor(sequence){
        this.sequence = sequence;
        this.hash = md5(sequence);
    }

    setUniprotData(uniprotData){
        this.uniprotData = uniprotData;
    }

    retrieveUniprotData(accession){
        let url = 'https://www.ebi.ac.uk/proteins/api/proteins/' + accession;
        let self = this;

        {
            return new Promise((resolve, reject) => {
                request
                    .get(url, (error, response, body) => {
                        if(error){
                            reject(error);
                        } else {
                            let protein = JSON.parse(body);

                            self.uniprotData = protein;
                            resolve(protein);
                        }
                    });
            });
        }
    }

    getUniprotData(){
        return this.uniprotData;
    }

    getUniprotAccession(){
        return this.uniprotData && this.uniprotData.accession
    }
}

fromFasta

function

 fromFasta() 

Option name	Type	Description
text	String	A string representing the FASTA input
alphabet	Number	A string representing the alphabet to use for validation. Valid alphabets include "IUPAC", "IUPAC2", "EXTENDED-IUPAC2", "PSI-BLAST". Default is "IUPAC".
return	Promise	A promise that in it's then clause accepts an array parameter which can be decomposed (then([p,r]): (p) being an array of Protein objects (r) being an array containing the raw FASTA sequences parsed Promise get's rejected (aka. catch clause) if some parsing error occurs.

function fromFasta(text, alphabet){
    if(typeof text !== 'string'){
        throw "Passed invalid object to parse function."
    }
    else if(text.length < 1){
        throw "Passed an empty string."
    }

    let sequences = [];

    // this flag get's updated when I'm reading a sequence. No comments should appear when I'm reading a sequence (see switch).
    let readingSequence = false;
    let readingHeaders = false;

    return new Promise((resolve, reject) => {
        text
        // Split line by line
            .split("\n")
            // Get rid of lines only containing spaces or tabs (or nothing)
            .filter(s => s.replace(/[\s|\t]+/,'').length > 0)
            // Perform switch on line output
            .forEach((line) => {
                switch(true){
                    // Marks beginning of sequence in common FASTA file
                    case /^>/.test(line):
                    // Comments can only appear in header. If ; appears while reading a sequence,
                    // am most likely starting to read a new protein which laks the usual > beginning.
                    // Be very strict about this condition.
                    case (/^;/.test(line) && readingSequence === true && readingHeaders === false):
                    // Case where ; sequence starts at beginning of file
                    case (/^;/.test(line) && readingSequence === false && readingHeaders === false):
                        sequences.push({
                            header: line.substring(1, line.length),
                            headerInfo: extractFASTAHeaderInfo(line),
                            sequence: '',
                            comments: ''
                        });

                        readingHeaders = true;
                        readingSequence = false;

                        break;

                    // Some sequences terminate in *. Get rid of that and update the reading sequence condition.
                    case FASTAEndReadParser(alphabet).test(line) && (
                        (readingSequence === false && readingHeaders === true) ||
                        (readingSequence === true && readingHeaders === false)
                    ):
                        sequences[sequences.length-1].sequence += line.substring(1, line.length-1);

                        readingSequence = false;

                        break;

                    // If repetition of characters, most likely sequence
                    // IMPORTANT!!! ONLY CAPITAL LETTERS!!!!
                    case FASTABodyParser(alphabet).test(line) && (
                        (readingSequence === false && readingHeaders === true) ||
                        (readingSequence === true && readingHeaders === false)
                    ):
                        sequences[sequences.length-1].sequence += line;

                        readingSequence = true;
                        readingHeaders = false;

                        break;

                    // If reading header and ; appears: it's a comment
                    case (/^;/.test(line) && readingSequence === false && readingHeaders === true):
                        sequences[sequences.length-1].comments += line.substring(1, line.length) + ' ';
                        break;

                    // Something weird happened!
                    default:
                        return reject("Could not parse one line of FASTA input:\n\n" + line);
                }
            });

        let promises = [];

        sequences.forEach(s => {
            promises.push(new Promise((resolve, reject) => {
                    let uniprotAccession = s.headerInfo.find(p => p.database === "sp");

                    if(uniprotAccession){
                        fromAccession(uniprotAccession.identifier)
                            .then(([proteins, _]) => {
                                resolve(proteins[0]);
                            })
                            .catch(() => resolve(new Protein(s.sequence)));
                    } else {
                        resolve(new Protein(s.sequence));
                    }
                })
            );
        });

        return Promise.all(promises)
            .then(proteins => resolve([proteins, sequences]))
            .catch(e => reject(e));
    });
}

fromAccession

function

 fromAccession() 

Option name	Type	Description
accession	String	A string representing the UniProt accession number (eg.: P12345)
return	Promise	A promise that in it's then clause accepts an array parameter which can be decomposed (then([p,r]): (p) being an array containing one Protein object (r) being an array containing one entry, aka. the raw GET result from UniProt Promise get's rejected (aka. catch clause) if 5 or 4 response from server.

function fromAccession(accession) {
    if(!accessionNumberRegex.test(accession)){
        return new Promise((resolve, reject) => {
            return reject();
        });
    }

    let url = 'https://www.ebi.ac.uk/proteins/api/proteins/' + accession;

    {
        return new Promise((resolve, reject) => {
            request
                .get(url, (error, response, body) => {
                    if(error){
                        return reject(error);
                    } else {
                        let protein = JSON.parse(body);
                        let p = new Protein(protein.sequence.sequence);
                        p.setUniprotData(protein);

                        return resolve([[p], [protein]]);
                    }
                });
        });
    }
}

fromUniprotQuery

function

 fromUniprotQuery() 

Option name	Type	Description
query	String	A string representing a protein name, a gene name, or anything UniProt-queriable
limit	Number	A number representing the max amount of returned sequences by the query. If omitted, defaults to 2. Set to undefined for no limit.
return	Promise	A promise that in it's then clause accepts an array parameter which can be decomposed (then([p,r]): (p) being an array of Protein objects (r) being an array containing the raw FASTA sequences parsed Promise get's rejected (aka. catch clause) if some parsing error occurs.

function fromUniprotQuery(query, limit=2) {

    // Limit to two entries: if more than 1, you know: identifier is not unique!
    let url = 'https://www.uniprot.org/uniprot/?format=fasta&limit=' + limit + '&query=' + query;

    if(limit === undefined){
        url = 'https://www.uniprot.org/uniprot/?format=fasta&query=' + query;
    }

    {
        return new Promise((resolve, reject) => {
            request
                .get(url, (error, response, fastaProteins) => {
                    if(error){
                        return reject(error);
                    } else {
                        if(fastaProteins.length > 0){
                            return fromFasta(fastaProteins, alphabets.IUPAC2)
                                .then(result => {
                                    resolve(result);
                                })
                                .catch(error => {
                                    reject(error);
                                });
                        } else {
                            return reject("No sequences found");
                        }
                    }
                });
        });
    }
}

fromSequence

function

 fromSequence() 

Option name	Type	Description
sequence	String	A string representing a protein sequence (A-Z)
alphabet	Number	A string representing the alphabet to use for validation. Valid alphabets include "IUPAC", "IUPAC2", "EXTENDED-IUPAC2", "PSI-BLAST". Default is "IUPAC".
return	Promise	A promise that in it's then clause accepts an array parameter which can be decomposed (then([p,r]): (p) being an array containing one Protein object (r) being an array containing one string representing the sequence matched Promise get's rejected (aka. catch clause) if parsing doesn't identify candidates

function fromSequence(sequence, alphabet) {
    return new Promise((resolve, reject) => {
        let match = sequence.match(sequenceParser(alphabet));
        if (match !== undefined && match !== null) {
            match = match.map(e => e.replace(/\n/g,""));

            return resolve([[new Protein(match[0])], [match[0]]]);
        } else {
            return reject('No sequence identified');
        }
    });
}

validInput

function

 validInput() 

Option name	Type	Description
text	String	A string representing a FASTA sequence, an UniProt accession or a sequence in A-Z format
alphabet	Number	A string representing the alphabet to use for validation. Valid alphabets include "IUPAC", "IUPAC2", "EXTENDED-IUPAC2", "PSI-BLAST". Default is "IUPAC".
return	Object	True if text can be parsed either as UniProt accession, AA sequence or FASTA file

function validInput(text, alphabet) {
    switch(true){
        case (accessionNumberRegex.test(text)):
            return parsers.accession;
        case sequenceParser(alphabet).test(text):
            return parsers.aa;
        case validFasta(text, alphabet):
            return parsers.fasta;
        case (uniprotNameRegex.test(text)):
            return parsers.protein_name;
        default:
            return undefined;
    }
}

autodetect

function

 autodetect() 

Option name	Type	Description
text	String	A string representing a FASTA sequence, an UniProt accession or a sequence in A-Z format
alphabet	Number	A string representing the alphabet to use for validation. Valid alphabets include "IUPAC", "IUPAC2", "EXTENDED-IUPAC2", "PSI-BLAST". Default is "IUPAC".
return	function	Returns the correct function to parse the text passed or undefined if text doesn't conform to any standard (AA, FASTA, UniProt Accession).

function autodetect(text, alphabet) {
    switch(true){
        case (accessionNumberRegex.test(text)):
            return fromAccession;
        case sequenceParser(alphabet).test(text):
            // Return nested function, so that alphabet is defined at this stage already (avoid inconsistency!)
            return (text) => fromSequence(text, alphabet);
        case validFasta(text, alphabet):
            // Return nested function, so that alphabet is defined at this stage already (avoid inconsistency!)
            return (text) => fromFasta(text, alphabet);
        case (uniprotNameRegex.test(text)):
            return fromUniprotQuery;
        default:
            return undefined;
    }
}

alphabets

declaration

 alphabets 

const alphabets = {
    "PSI_BLAST" : 0,
    "EXTENDED_IUPAC2": 1,
    "IUPAC2": 2,
    "IUPAC": 3,
    "NATURAL": 4,
};

parsers

declaration

 parsers 

const parsers = {
    fasta: 0,
    aa: 1,
    accession: 2,
    protein_name: 3,
    uniprot: 4
};

exports.Protein = Protein;
exports.fromFasta = fromFasta;
exports.fromAccession = fromAccession;
exports.fromUniprotQuery = fromUniprotQuery;
exports.fromSequence = fromSequence;
exports.validInput = validInput;
exports.autodetect = autodetect;
exports.alphabets = alphabets;
exports.parsers = parsers;