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    gitax

    0.0.6 • Public • Published

    gitax

    gitax fetches taxonomy_id,names from given NCBI gi.

    installation

    $ npm install -g gitax

    usage

    command line

    gi=1234567
    tax_id=$(gitax $gi /path/to/gi_tax_nucl.dmp)
    echo $tax_id

    with taxonomy names

    gi=1234567
    gitax $gi /path/to/gi_tax_nucl.dmp --names /path/to/names.dmp

    set default files

    gitax_set /path/to/gi_tax_nucl.dmp --names /path/to/names.dmp
     
    # run without gi_tax_nucl 
    gitax 1234567
     
    # unset 
    gitax_set

    JavaScript API

    gitax = require("gitax")
    tax_id = gitax(1234567, "/path/to/gi_tax_nucl.dmp");

    with taxonomy names

    gitax = require("gitax")
    taxinfo = gitax(1234567, "/path/to/gi_tax_nucl.dmp", "/path/to/names.dmp");
    console.log(taxinfo.tax_id); // taxonomy id
    console.log(taxinfo.names); // taxonomy names // array of [name, uniq_name, name_class]

    gi_tax_nucl.dmp?

    a file which describes relations between gi and taxonomy_id

    download one from ftp://ftp.ncbi.nih.gov/pub/taxonomy/

    names.dmp?

    a file which describes relations between gi and taxonomy_id

    downloaded with gi_tax_nucl.dmp (from ftp://ftp.ncbi.nih.gov/pub/taxonomy/)

    wget -r ftp://ftp.ncbi.nih.gov/pub/taxonomy/

    Install

    npm i gitax

    DownloadsWeekly Downloads

    8

    Version

    0.0.6

    License

    none

    Last publish

    Collaborators

    • shinout