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    genomediff

    1.7.1 • Public • Published

    Genomediff

    Travis build status Dependency Status

    Parses strings from files in the GenomeDiff format generated by the breseq variant caller for haploid microbial organisms.

    Installation


    $(node bin)/npm install genomediff

    Note: It has only been tested with Node 5.

    Usage


    GenomeDiff strings are parsed using GenomeDiff.parse(<string>). The GenomeDiff object contains a metadata dict with the meta data, as well as mutations, evidence and validation lists, each containing records of that type. Records can be accessed through this list or by id using GenomeDiff.parse(<string>)[<id>]. GenomeDiff is an iterable and iterating it will return all properties and records.

    For accessing all the records you can use GenomeDiff.parse('<string>').values() which returns an iterable but only with the Record types.

    For accessing the parents of a specific mutation you can use the parents property available on each record:

    let doc = GenomeDiff.parse('<string>'); // a genomediff string
    let someMutation = doc[12]; // mutation with id '12'
    someMutation.parents // this will lookup all the parents of the record with id `12` and return as an array of Records

    If you want to get an attribute from a parent record then you can use the .get(<attribute>) method available on the record to do so:

    let doc = GenomeDiff.parse('<string>'); // a genomediff string
    let someMutation = doc[12]; // mutation with id '12'
    someMutation.get('coverage') // this will lookup all the parents of the record with id `12` and return the value of the attribute `coverage` if found on any of the parent records

    If used with node, you can use the following:

    var GenomeDiff = require('genomediff').GenomeDiff;
    var fs = require('fs');
    var file = fs.readFileSync('<path>', "utf8"); // path to your `.gd` file
    var doc = GenomeDiff.parse(file);

    If used in a browser, use:

    import {GenomeDiff} from 'genomediff';
    var doc = GenomeDiff.parse('<string>'); // a genomediff string

    Note: Keep in mind that this package requires an ES6 environment in order to work.

    Running Tests


    A full test suite can be run using npm test. If you wish to run tests on file change, use jasmine-node dist/ --autotest --color --verbose.

    Development


    When developing, use tsc --watch to build the .ts files on change. Alternatively, you can use npm run build if you do not wish to run the build on file change.

    Note: If you add new files or remove files, make sure to edit the "files" field in tsconfig.json:

    "files": [
        "./typings/typings.d.ts", // never remove this line
        // add more files after this line
        "./src/parser.ts",
        "./src/parser.spec.ts",
        "./src/records.ts",
        "./src/records.spec.ts",
        "./src/gd.ts",
        "./src/gd.spec.ts"
    ]

    Install

    npm i genomediff

    DownloadsWeekly Downloads

    31

    Version

    1.7.1

    License

    MIT

    Last publish

    Collaborators

    • lyschoening
    • rolandjitsu