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    sgd_visualizationpublic

    SGD Visualization

    Build Status

    This is a set of react components used for genomic data visualization by SGD.

    Usage

    See examples directory for example configuration values.

    as a React plugin

    React.render(React.createElement(_VariantViewerComponent, {
        name: "ACT1",
        strand: "+",
        chromStart: 53260,
        chromEnd: 54696,
        blockStarts: [0, 320],
        blockSizes: [10, 1117],
        dnaLength: 1437,
        contigName: "Chromosome VI",
        contigHref: "http://yeastgenome.org/contig/Chromosome_VI/overview",
        alignedDnaSequences: [
            {
                id: 1,
                name: "S288C",
                href: "http://yeastgenome.org/strain/S288C/overview",
                sequence: "ATGGATTCTGGTATGTTCTAGCGCTTGCACCATCCCATTTAACTGTAAGAAGAATTGCACGGTCCCAATTGCTCGAGAGATTTCTCTTTTACCTTTTTTTACTATTTTTCACTCTCCCATAACCTCCTATATTGACTGATCTGTAATAACCACGATATTATTGGAATAAATAGGGGCTTGAAATTTGGAAAAAAAAAAAAAACTGAAATATTTTCGTGATAAGTGATAGTGATATTCTTCTTTTATTTGCTACTGTTACTAAGTCTCATGTACTAACATCGATTGCTTCATTCTTTTTGTTGCTATATTATATGTTTAGAGGTTGCTGCTTTGGTTATTGATAACGGTTCTGGTATGTGTAAAGCCGGTTTTGCCGGTGACGACGCTCCTCGTGCTGTCTTCCCATCTATCGTCGGTAGACCAAGACACCAAGGTATCATGGTCGGTATGGGTCAAAAAGACTCCTACGTTGGTGATGAAGCTCAATCCAAGAGAGGTATCTTGACTTTACGTTACCCAATTGAACACGGTATTGTCACCAACTGGGACGATATGGAAAAGATCTGGCATCATACCTTCTACAACGAATTGAGAGTTGCCCCAGAAGAACACCCTGTTCTTTTGACTGAAGCTCCAATGAACCCTAAATCAAACAGAGAAAAGATGACTCAAATTATGTTTGAAACTTTCAACGTTCCAGCCTTCTACGTTTCCATCCAAGCCGTTTTGTCCTTGTACTCTTCCGGTAGAACTACTGGTATTGTTTTGGATTCCGGTGATGGTGTTACTCACGTCGTTCCAATTTACGCTGGTTTCTCTCTACCTCACGCCATTTTGAGAATCGATTTGGCCGGTAGAGATTTGACTGACTACTTGATGAAGATCTTGAGTGAACGTGGTTACTCTTTCTCCACCACTGCTGAAAGAGAAATTGTCCGTGACATCAAGGAAAAACTATGTTACGTCGCCTTGGACTTCGAACAAGAAATGCAAACCGCTGCTCAATCTTCTTCAATTGAAAAATCCTACGAACTTCCAGATGGTCAAGTCATCACTATTGGTAACGAAAGATTCAGAGCCCCAGAAGCTTTGTTCCATCCTTCTGTTTTGGGTTTGGAATCTGCCGGTATTGACCAAACTACTTACAACTCCATCATGAAGTGTGATGTCGATGTCCGTAAGGAATTATACGGTAACATCGTTATGTCCGGTGGTACCACCATGTTCCCAGGTATTGCCGAAAGAATGCAAAAGGAAATCACCGCTTTGGCTCCATCTTCCATGAAGGTCAAGATCATTGCTCCTCCAGAAAGAAAGTACTCCGTCTGGATTGGTGGTTCTATCTTGGCTTCTTTGACTACCTTCCAACAAATGTGGATCTCAAAACAAGAATACGACGAAAGTGGTCCATCTATCGTTCACCACAAGTGTTTCTAA"
            },
            {
                id: 13,
                name: "RM11-1a",
                href: "http://yeastgenome.org/strain/RM11-1a/overview",
                sequence: "------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGTGTAAAGCCGGTTTTGCCGGTGACGACGCTCCTCGTGCTGTCTTCCCATCTATCGTCGGTAGACCAAGACACCAAGGTATCATGGTCGGTATGGGTCAAAAAGACTCCTACGTTGGTGATGAAGCTCAATCCAAGAGAGGTATCTTGACTTTACGTTACCCAATTGAACACGGTATTGTCACCAACTGGGACGATATGGAAAAGATCTGGCATCATACCTTCTACAACGAATTGAGAGTTGCCCCAGAAGAACACCCTGTTCTTTTGACTGAAGCTCCAATGAACCCTAAATCAAACAGAGAAAAGATGACTCAAATTATGTTTGAAACTTTCAACGTTCCAGCCTTCTATGTTTCCATCCAAGCCGTTTTGTCCTTGTACTCTTCCGGTAGAACTACTGGTATTGTTTTGGATTCCGGTGATGGTGTTACTCACGTCGTTCCAATTTACGCTGGTTTCTCTCTACCTCACGCCATTTTGAGAATCGATTTGGCCGGTAGAGATTTGACTGACTACTTGATGAAGATCTTGAGTGAACGTGGTTACTCTTTCTCCACCACTGCTGAAAGAGAAATTGTCCGTGACATCAAGGAAAAACTATGTTACGTCGCCTTGGACTTCGAACAAGAAATGCAAACCGCTGCTCAATCTTCTTCAATTGAAAAATCCTACGAACTTCCAGATGGTCAAGTCATCACTATTGGTAACGAAAGATTCAGAGCCCCAGAAGCTTTGTTCCATCCTTCTGTTTTGGGTTTGGAATCTGCCGGTATTGACCAAACTACTTACAACTCCATCATGAAGTGTGATGTCGATGTCCGTAAGGAATTATACGGTAACATCGTTATGTCCGGTGGTACCACCATGTTCCCAGGTATTGCCGAAAGAATGCAAAAGGAAATCACCGCTTTGGCTCCATCTTCCATGAAGGTCAAGATCATTGCTCCTCCAGAAAGAAAGTACTCCGTCTGGATTGGTGGTTCTATCTTGGCTTCTTTGACTACCTTCCAACAAATGTGGATCTCAAAACAAGAATACGACGAAAGTGGTCCATCTATCGTTCACCACAAGTGTTTCTAA"
            },
            {
                id: 9,
                name: "Y55",
                href: "http://yeastgenome.org/strain/y55/overview",
                sequence: "------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGTGTAAAGCCGGTTTTGCCGGTGACGACGCTCCTCGTGCTGTCTTCCCATCTATCGTCGGTAGACCAAGACACCAAGGTATCATGGTCGGTATGGGTCAAAAAGACTCCTACGTTGGTGATGAAGCTCAATCCAAGAGAGGTATCTTGACTTTACGTTACCCAATTGAACACGGTATTGTCACCAACTGGGACGATATGGAAAAGATCTGGCATCATACCTTCTACAACGAATTGAGAGTTGCCCCAGAAGAACACCCTGTTCTTTTGACTGAAGCTCCAATGAACCCTAAATCAAACAGAGAAAAGATGACTCAAATTATGTTTGAAACTTTCAACGTTCCAGCCTTCTACGTTTCCATCCAAGCCGTTTTGTCCTTGTACTCTTCCGGTAGAACTACTGGTATTGTTTTGGATTCCGGTGATGGTGTTACTCACGTCGTTCCAATTTACGCTGGTTTCTCTCTACCTCACGCCATTTTGAGAATCGATTTGGCCGGTAGAGATTTGACTGACTACTTGATGAAGATCTTGAGTGAACGTGGTTACTCTTTCTCCACCACTGCTGAAAGAGAAATTGTCCGTGACATCAAGGAAAAACTATGTTACGTCGCCTTGGACTTCGAACAAGAAATGCAAACCGCTGCTCAATCTTCTTCAATTGAAAAATCCTACGAACTTCCAGATGGTCAAGTCATCACTATTGGTAACGAAAGATTCAGAGCCCCAGAAGCTTTGTTCCATCCTTCTGTTTTGGGTTTGGAATCTGCCGGTATTGACCAAACTACTTACAACTCCATCATGAAGTGTGATGTCGATGTCCGTAAGGAATTATACGGTAACATCGTTATGTCCGGTGGTACCACCATGTTCCCAGGTATTGCCGAAAGAATGCAAAAGGAAATCACCGCTTTGGCTCCATCTTCCATGAAGGTCAAGATCATCGCTCCTCCAGAAAGAAAGTACTCCGTCTGGATTGGTGGTTCTATCTTGGCTTCTTTGACTACCTTCCAACAAATGTGGATCTCAAAACAAGAATACGACGAAAGTGGTCCATCTATCGTTCACCACAAGTGTTTCTAA"
            }
        ],
        variantDataDna: [
            {
                start: 1,
                variant_type: "Deletion",
                score: 11,
                end: 355
            },
            {
                snpType: "Synonymous",
                start: 708,
                variant_type: "SNP",
                score: 4,
                end: 709
            },
            {
                snpType: "Synonymous",
                start: 1299,
                variant_type: "SNP",
                score: 2,
                end: 1300
            }
        ],
        variantDataProtein: null,
        proteinLength: null,
        alignedProteinSequences: null,
        domains: null,
        isProteinMode: false,
        downloadCaption: "SGD 2015 Stanford University"
    });

    or as a standalone library

    var VariantViewer = require("sgd_visualization").VariantViewer;
    var vv = new VariantViewer({
        el: document.getElementById("target"),
        config: {
            name: "ACT1",
            strand: "+",
            chromStart: 53260,
            chromEnd: 54696,
            blockStarts: [0, 320],
            blockSizes: [10, 1117],
            dnaLength: 1437,
            contigName: "Chromosome VI",
            contigHref: "http://yeastgenome.org/contig/Chromosome_VI/overview",
            alignedDnaSequences: [
                {
                    id: 1,
                    name: "S288C",
                    href: "http://yeastgenome.org/strain/S288C/overview",
                    sequence: "ATGGATTCTGGTATGTTCTAGCGCTTGCACCATCCCATTTAACTGTAAGAAGAATTGCACGGTCCCAATTGCTCGAGAGATTTCTCTTTTACCTTTTTTTACTATTTTTCACTCTCCCATAACCTCCTATATTGACTGATCTGTAATAACCACGATATTATTGGAATAAATAGGGGCTTGAAATTTGGAAAAAAAAAAAAAACTGAAATATTTTCGTGATAAGTGATAGTGATATTCTTCTTTTATTTGCTACTGTTACTAAGTCTCATGTACTAACATCGATTGCTTCATTCTTTTTGTTGCTATATTATATGTTTAGAGGTTGCTGCTTTGGTTATTGATAACGGTTCTGGTATGTGTAAAGCCGGTTTTGCCGGTGACGACGCTCCTCGTGCTGTCTTCCCATCTATCGTCGGTAGACCAAGACACCAAGGTATCATGGTCGGTATGGGTCAAAAAGACTCCTACGTTGGTGATGAAGCTCAATCCAAGAGAGGTATCTTGACTTTACGTTACCCAATTGAACACGGTATTGTCACCAACTGGGACGATATGGAAAAGATCTGGCATCATACCTTCTACAACGAATTGAGAGTTGCCCCAGAAGAACACCCTGTTCTTTTGACTGAAGCTCCAATGAACCCTAAATCAAACAGAGAAAAGATGACTCAAATTATGTTTGAAACTTTCAACGTTCCAGCCTTCTACGTTTCCATCCAAGCCGTTTTGTCCTTGTACTCTTCCGGTAGAACTACTGGTATTGTTTTGGATTCCGGTGATGGTGTTACTCACGTCGTTCCAATTTACGCTGGTTTCTCTCTACCTCACGCCATTTTGAGAATCGATTTGGCCGGTAGAGATTTGACTGACTACTTGATGAAGATCTTGAGTGAACGTGGTTACTCTTTCTCCACCACTGCTGAAAGAGAAATTGTCCGTGACATCAAGGAAAAACTATGTTACGTCGCCTTGGACTTCGAACAAGAAATGCAAACCGCTGCTCAATCTTCTTCAATTGAAAAATCCTACGAACTTCCAGATGGTCAAGTCATCACTATTGGTAACGAAAGATTCAGAGCCCCAGAAGCTTTGTTCCATCCTTCTGTTTTGGGTTTGGAATCTGCCGGTATTGACCAAACTACTTACAACTCCATCATGAAGTGTGATGTCGATGTCCGTAAGGAATTATACGGTAACATCGTTATGTCCGGTGGTACCACCATGTTCCCAGGTATTGCCGAAAGAATGCAAAAGGAAATCACCGCTTTGGCTCCATCTTCCATGAAGGTCAAGATCATTGCTCCTCCAGAAAGAAAGTACTCCGTCTGGATTGGTGGTTCTATCTTGGCTTCTTTGACTACCTTCCAACAAATGTGGATCTCAAAACAAGAATACGACGAAAGTGGTCCATCTATCGTTCACCACAAGTGTTTCTAA"
                },
                {
                    id: 13,
                    name: "RM11-1a",
                    href: "http://yeastgenome.org/strain/RM11-1a/overview",
                    sequence: "------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGTGTAAAGCCGGTTTTGCCGGTGACGACGCTCCTCGTGCTGTCTTCCCATCTATCGTCGGTAGACCAAGACACCAAGGTATCATGGTCGGTATGGGTCAAAAAGACTCCTACGTTGGTGATGAAGCTCAATCCAAGAGAGGTATCTTGACTTTACGTTACCCAATTGAACACGGTATTGTCACCAACTGGGACGATATGGAAAAGATCTGGCATCATACCTTCTACAACGAATTGAGAGTTGCCCCAGAAGAACACCCTGTTCTTTTGACTGAAGCTCCAATGAACCCTAAATCAAACAGAGAAAAGATGACTCAAATTATGTTTGAAACTTTCAACGTTCCAGCCTTCTATGTTTCCATCCAAGCCGTTTTGTCCTTGTACTCTTCCGGTAGAACTACTGGTATTGTTTTGGATTCCGGTGATGGTGTTACTCACGTCGTTCCAATTTACGCTGGTTTCTCTCTACCTCACGCCATTTTGAGAATCGATTTGGCCGGTAGAGATTTGACTGACTACTTGATGAAGATCTTGAGTGAACGTGGTTACTCTTTCTCCACCACTGCTGAAAGAGAAATTGTCCGTGACATCAAGGAAAAACTATGTTACGTCGCCTTGGACTTCGAACAAGAAATGCAAACCGCTGCTCAATCTTCTTCAATTGAAAAATCCTACGAACTTCCAGATGGTCAAGTCATCACTATTGGTAACGAAAGATTCAGAGCCCCAGAAGCTTTGTTCCATCCTTCTGTTTTGGGTTTGGAATCTGCCGGTATTGACCAAACTACTTACAACTCCATCATGAAGTGTGATGTCGATGTCCGTAAGGAATTATACGGTAACATCGTTATGTCCGGTGGTACCACCATGTTCCCAGGTATTGCCGAAAGAATGCAAAAGGAAATCACCGCTTTGGCTCCATCTTCCATGAAGGTCAAGATCATTGCTCCTCCAGAAAGAAAGTACTCCGTCTGGATTGGTGGTTCTATCTTGGCTTCTTTGACTACCTTCCAACAAATGTGGATCTCAAAACAAGAATACGACGAAAGTGGTCCATCTATCGTTCACCACAAGTGTTTCTAA"
                },
                {
                    id: 9,
                    name: "Y55",
                    href: "http://yeastgenome.org/strain/y55/overview",
                    sequence: "------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGTGTAAAGCCGGTTTTGCCGGTGACGACGCTCCTCGTGCTGTCTTCCCATCTATCGTCGGTAGACCAAGACACCAAGGTATCATGGTCGGTATGGGTCAAAAAGACTCCTACGTTGGTGATGAAGCTCAATCCAAGAGAGGTATCTTGACTTTACGTTACCCAATTGAACACGGTATTGTCACCAACTGGGACGATATGGAAAAGATCTGGCATCATACCTTCTACAACGAATTGAGAGTTGCCCCAGAAGAACACCCTGTTCTTTTGACTGAAGCTCCAATGAACCCTAAATCAAACAGAGAAAAGATGACTCAAATTATGTTTGAAACTTTCAACGTTCCAGCCTTCTACGTTTCCATCCAAGCCGTTTTGTCCTTGTACTCTTCCGGTAGAACTACTGGTATTGTTTTGGATTCCGGTGATGGTGTTACTCACGTCGTTCCAATTTACGCTGGTTTCTCTCTACCTCACGCCATTTTGAGAATCGATTTGGCCGGTAGAGATTTGACTGACTACTTGATGAAGATCTTGAGTGAACGTGGTTACTCTTTCTCCACCACTGCTGAAAGAGAAATTGTCCGTGACATCAAGGAAAAACTATGTTACGTCGCCTTGGACTTCGAACAAGAAATGCAAACCGCTGCTCAATCTTCTTCAATTGAAAAATCCTACGAACTTCCAGATGGTCAAGTCATCACTATTGGTAACGAAAGATTCAGAGCCCCAGAAGCTTTGTTCCATCCTTCTGTTTTGGGTTTGGAATCTGCCGGTATTGACCAAACTACTTACAACTCCATCATGAAGTGTGATGTCGATGTCCGTAAGGAATTATACGGTAACATCGTTATGTCCGGTGGTACCACCATGTTCCCAGGTATTGCCGAAAGAATGCAAAAGGAAATCACCGCTTTGGCTCCATCTTCCATGAAGGTCAAGATCATCGCTCCTCCAGAAAGAAAGTACTCCGTCTGGATTGGTGGTTCTATCTTGGCTTCTTTGACTACCTTCCAACAAATGTGGATCTCAAAACAAGAATACGACGAAAGTGGTCCATCTATCGTTCACCACAAGTGTTTCTAA"
                }
            ],
            variantDataDna: [
                {
                    start: 1,
                    variant_type: "Deletion",
                    score: 11,
                    end: 355
                },
                {
                    snpType: "Synonymous",
                    start: 708,
                    variant_type: "SNP",
                    score: 4,
                    end: 709
                },
                {
                    snpType: "Synonymous",
                    start: 1299,
                    variant_type: "SNP",
                    score: 2,
                    end: 1300
                }
            ],
            variantDataProtein: null,
            proteinLength: null,
            alignedProteinSequences: null,
            domains: null,
            isProteinMode: false,
            downloadCaption: "SGD 2015 Stanford University"
        }
    });

    See Examples

    Clone the repo, make sure sniper is installed.

    Install dependencies

    $ npm install
    

    Run example server

    $ sniper
    

    Go to http://localhost:9090/examples/variant_viewer

    Look at examples/protein_viewer/index.html to see how the protein viewer is configured.

    Run Tests

    Install mocha and then run

    $ mocha
    

    License

    The MIT License

    Copyright (c) 2015, Travis Sheppard

    Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

    The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

    install

    npm i sgd_visualization

    Downloadsweekly downloads

    0

    version

    1.0.12

    license

    none

    repository

    githubgithub

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