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    txreaderpublic

    txreader

    description

    Handling transcript information data. (Node.js) (e.g. knownGene.txt)

    installation

    $ npm install txreader
    

    dependencies

    usage

    create an instance

    var tx = TxReader.create('knownGene.txt', {
      xref: 'kgXref.txt' // gene name info (optional)
    });
    

    get info from ucsc transcript id

    var info = tx.getInfo('uc001acn.2'); // info object (explains later)
    

    get ucsc transcripts ids from gene name

    var BCRs = tx.getTxsByGene('BCR');
    

    get ucsc transcript ids from refseq id

    var NMs  = tx.getTxsByRefSeqId('NM_033487'); // get list of transcripts whose refseq id is 'NM_033487'
    

    API Documentation

    • TxReader.create(knownGene, options)
    • txr.getTxsByExon(formattedExon)
    • txr.getTxsByGene(geneName)
    • txr.getTxsByRefSeqId(refseqId)
    • txr.getNames()
    • txr.getGeneName(txname)
    • txr.getRefSeqId(txname)
    • txr.getInfo(name)
    • txr.getExons(name)
    • txr.getSeq(name, fr, options)
    • TxReader.parseLine(line)

    TxReader.create(knownGene, options)

    Creates an instance of TxReader.

    knownGene is a file UCSC provides. The file format is in http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz

    options is option object.

    key description example
    xref xref file (compatible with http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/kgXref.txt.gz ) kgXref.txt
    noCacheInfo if true, not caching transcript information true

    txr.getInfo(name)

    Gets an information object of a transcript.

    name is a name of transcript.

    Returns information object, following the format.

    key name description example
    name name of the transcript uc011msz.1
    chrom chromosome name chr11
    strand strand of the transcript (+/-) +
    isMinus if strand is minus (boolean) false
    txStart transcription start position (0-based coordinate system) 12345880
    txEnd transcription end position (0-based coordinate system) 12346880
    cdsStart coding region start position (0-based coordinate system) 12345880
    cdsEnd coding region end position (0-based coordinate system) 12346880
    proteinID protein ID B7ZGX9
    exons list of exons order by exon num. (0-based coordinate) [{chr: xxx, start: xxx, end: xxx, strand: xxx}, ...]
    gene gene name ALG13
    refseqId refseq ID NM_033487

    txr.getSeq(name, fr, options)

    Gets sequences of given name.

    name is a UCSC transcript.

    fr is a instance of fastareader.

    options is as follows.

    key name description default example
    startExon start exon number 1 2
    startBase start base in the start exon(0-based coordinate) 0 21
    endExon end exon number (exons.length) 4
    endBase end base in the end exon(0-based coordinate) (exon length of the endExon) 300

    txr.getNames()

    Gets a list of all transcripts.

    txr.getTxsByExon(formattedExon)

    Gets a hash of transcript which has the given exon.

    formattedExon is compatible with dna library

    chr2:34100214-34101989,-
    

    Returns a hash whose keys are UCSC transcript id and values are the exon number.

    txr.getTxsByGene(geneName)

    Gets a list of UCSC transcripts whose gene name is geneName.

    geneName must be compatible with one written in options.xref file.

    txr.getTxsByRefSeqId(refseqId)

    Gets a list of UCSC transcripts whose gene name is geneName.

    refseqId must be compatible with one written in options.xref file.

    TxReader.parseLine(line)

    (static) Parses a line from UCSC knownGene file. Returns information object (written in txr.getInfo()).

    Keywords

    none

    install

    npm i txreader

    Downloadsweekly downloads

    49

    version

    0.1.1

    license

    none

    last publish

    collaborators

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