Bioinformatics plugin for nushell.

Overview

Nushell bio

A bioinformatics plugin for nushell. The aim initially is to create a bunch of parsers for all of the common bioinformatics file formats and take it from there!

Quick setup

Go and get nushell, it's great. I'm assuming you have the rust toolchain installed. Then come back!

# clone this repo
git clone https://github.com/Euphrasiologist/nu_plugin_bio
# build
cargo build --release
# register the plugin
register nu_plugin_bio/target/release/nu_plugin_bio

# parse a fasta!
open ./tests/test.fasta

Aims

Aim to support the following:

  • BAM 1.6
  • BCF 2.2
  • BED
  • BGZF (gzipped versions of all file formats.)
  • CRAM 3.0
  • FASTA
  • FASTQ
  • GFF3
  • GTF 2.2
  • SAM 1.6
  • tabix
  • VCF 4.3
  • GFA v1 (https://github.com/chfi/rs-gfa)

Plus maybe some generic functions such as:

  • indexing
  • viewing
  • getting headers
  • counting lengths
  • changing between file formats
Comments
  • Getting the below error for Different Maps

    Getting the below error for Different Maps

    image

    Code // STEP 1 - Include Dependencies

    // Include react import React from 'react'; // import ReactDOM from 'react-dom'; // Step 1 - Including react // import React from 'react'; // import ReactDOM from 'react-dom';

    // Step 2 - Including the react-fusioncharts component import ReactFC from 'react-fusioncharts';

    // Step 3 - Including the fusioncharts library import FusionCharts from 'fusioncharts';

    // Step 4 - Including the map renderer import FusionMaps from 'fusioncharts/fusioncharts.maps';

    // Step 5 - Including the map definition file import California from 'fusionmaps/maps/fusioncharts.california';

    // Step 6 - Including the theme as fusion import FusionTheme from 'fusioncharts/themes/fusioncharts.theme.fusion';

    // Step 7 - Adding the map and theme as dependency to the core fusioncharts ReactFC.fcRoot(FusionCharts, FusionMaps, California, FusionTheme);

    //Step 8 - Defining map data const mapData = [{ "id": "001", "value": 2834 }, { "id": "003", "value": 3182 }, { "id": "005", "value": 3280 }, { "id": "007", "value": 911 }, { "id": "009", "value": 292 }, { "id": "011", "value": 530 }, { "id": "013", "value": 2515 }, { "id": "015", "value": 728 }, { "id": "017", "value": 1974 }, { "id": "019", "value": 848 }, { "id": "021", "value": 3278 }, { "id": "023", "value": 4463 }, { "id": "025", "value": 1198 }, { "id": "027", "value": 378 }, { "id": "029", "value": 2610 }, { "id": "031", "value": 1200 }, { "id": "033", "value": 3820 }, { "id": "035", "value": 940 }, { "id": "037", "value": 3416 }, { "id": "039", "value": 4004 }, { "id": "041", "value": 1604 }, { "id": "043", "value": 4011 }, { "id": "045", "value": 3203 }, { "id": "047", "value": 3775 }, { "id": "049", "value": 2721 }, { "id": "051", "value": 3417 }, { "id": "053", "value": 1530 }, { "id": "055", "value": 412 }, { "id": "057", "value": 3434 }, { "id": "059", "value": 1670 }, { "id": "061", "value": 1274 }, { "id": "063", "value": 4339 }, { "id": "065", "value": 2073 }, { "id": "067", "value": 1018 }, { "id": "069", "value": 3967 }, { "id": "071", "value": 3401 }, { "id": "073", "value": 3307 }, { "id": "075", "value": 1938 }, { "id": "077", "value": 489 }, { "id": "079", "value": 3207 }, { "id": "081", "value": 2295 }, { "id": "083", "value": 2747 }, { "id": "085", "value": 1114 }, { "id": "087", "value": 3400 }, { "id": "089", "value": 784 }, { "id": "091", "value": 1673 }, { "id": "093", "value": 4274 }, { "id": "095", "value": 4509 }, { "id": "097", "value": 3862 }, { "id": "099", "value": 1356 }, { "id": "101", "value": 4126 }, { "id": "103", "value": 1314 }, { "id": "105", "value": 1807 }, { "id": "107", "value": 4026 }, { "id": "109", "value": 3456 }, { "id": "111", "value": 1393 }, { "id": "113", "value": 1500 }, { "id": "115", "value": 2218 }]

    const colorrange = { "minvalue": "0", "startlabel": "Low", "endlabel": "High", "code": "e44a00", "gradient": "1", "color": [{ "maxvalue": "2500", "code": "f8bd19" }, { "maxvalue": "5000", "code": "6baa01" }] };

    // Step 9 - Creating the JSON object to store the map configurations const chartConfigs = { type: 'maps/northcarolina', width: '1000', height: '1000', dataFormat: 'json', dataSource: { "chart": { "animation": "0", "showbevel": "0", "usehovercolor": "1", "showlegend": "1", "legendposition": "BOTTOM", "legendborderalpha": "0", "legendbordercolor": "ffffff", "legendallowdrag": "0", "legendshadow": "0", "caption": "Website Visits for the month of March 2018", "connectorcolor": "000000", "fillalpha": "80", "hovercolor": "CCCCCC", "theme": "fusion" }, "colorrange": colorrange, "data": mapData } }; // Step 10 - Creating the DOM element to pass the react-fusioncharts component class Test extends React.Component { render() { return ( <ReactFC {...chartConfigs} /> ); } }

    // export default App

    export default Test;

    opened by vishals9711 147
  • Chart Type World, annotation label doesn't support styling.

    Chart Type World, annotation label doesn't support styling.

    I am trying to style the label for annotations of chart type world, the styling in tooltext is possible and I was able to customize it, however when I try to do same it randers all html as string. Surprisingly </br> tag does work on label. below is the sample what I want to achieve

    image

    I want to make the font of first line bigger and bold in the label.

    help wanted 
    opened by jeetendra-choudhary 11
  • Can build project because of fusioncharts

    Can build project because of fusioncharts

    I am developing react project created by create-react-app. I don't use webpack. just project created by create-react-app.

    Now I want to build using "npm run build", but i can't because of the error following:

    Failed to minify the code from this file:

        ./node_modules/fusioncharts/_internal/lib/lib.js:1:9788
    
    opened by ShininingLancer 9
  • window not defined when start

    window not defined when start

    I added a chart from Fusioncharts (this is chart: https://www.fusioncharts.com/charts/gauges/rating-meter-gauge) as a new dependency and trying to start the app it throws the following error and aborts: ReferenceError: window is not defined at Object. (/Users/phunghoang/Desktop/StockbookWebNew/node_modules/fusioncharts/fusioncharts.js:13:961) I followed these step: Install FusionCharts from npm $ npm install react-fusioncharts --save $ npm install fusioncharts --save My Project using Reactjs and Nextjs. Sorry My english not good?

    help wanted 
    opened by pxhoang1992 9
  • Pie chart labels and legends are not getting displayed properly - UI is getting disturbed - Intermittent issue.

    Pie chart labels and legends are not getting displayed properly - UI is getting disturbed - Intermittent issue.

    On load, Sometimes it does not display the labels until user clicks on the pie chart or legends. Sometimes, Even though labels gets displayed, UI gets disturbed(labels and legends' text). This is mostly happening on chrome and not Firefox.

    It will be helpful if anyone can suggest any change or solution.

    help wanted 
    opened by mayura-gslab 4
  • Import Modules

    Import Modules

    Hi, I get console error sometimes. "Uncaught TypeError: a.setChartData is not a function", as I observed this happens when the 3 module is about to regenerate on importing modules

    import React from 'react'; import ReactDOM from 'react-dom'; import ReactFC from 'react-fusioncharts';

    // Here import licensed version of FusionCharts import FusionCharts from './path/to/fusioncharts'; import Charts from './path/to/fusioncharts/fusioncharts.charts';

    // Provide FusionCharts core and other modules to resolve ReactFC.fcRoot(FusionCharts, Charts)

    , so my is this, although my page still running and execute the charts correctly even this error console showed, but there are times that it cause to break my page.

    opened by octal-laurence 3
  • tooltip and chart line/bar clicks not working

    tooltip and chart line/bar clicks not working

    I've created the following component, and when I import this component into another react component, it renders just fine, but the tooltips do not show and the event clicks on a bar or line do not work either. Is this a bug?

    `import FusionCharts from 'fusioncharts'; import charts from 'fusioncharts/fusioncharts.charts'; import ReactFC from 'react-fusioncharts'; charts(FusionCharts);

    export default class test extends React.Component { constructor(props) { super(props); }

    render() {
    	let myDataSource = {
    		chart: {
    			caption: "Harry's SuperMart",
    			subCaption: "Top 5 stores in last month by revenue",
    			numberPrefix: "$",
    			theme: "ocean"
    		},
    		data: [{
    			label: "Bakersfield Central",
    			value: "880000"
    		}, {
    			label: "Garden Groove harbour",
    			value: "730000"
    		}, {
    			label: "Los Angeles Topanga",
    			value: "590000"
    		}, {
    			label: "Compton-Rancho Dom",
    			value: "520000"
    		}, {
    			label: "Daly City Serramonte",
    			value: "330000"
    		}]
    	};
    
    let chartConfigs = {
        id: "revenue-chart2",
        renderAt: "revenue-chart-container2",
        type: "column2d",
        width: 500,
        height: 400,
        dataFormat: "json",
        dataSource: myDataSource,
        events: {
            dataplotclick: function (ev, props) {
                document.getElementById("value").innerHTML = props.displayValue;
            }
        }
    };
    
    	return (<ReactFC { ...chartConfigs } />);
    }
    

    }`

    opened by mclarentgp 2
  • Chart Type World, label unexpected border displayed.

    Chart Type World, label unexpected border displayed.

    The world map label shows an unexpected rounded border. The html element which gets generated at runtime is as below -

    <rect x="629.40625" y="257" width="62.828125" height="31.15625" ry="10" rx="10" fill="none" stroke="#666666" stroke-opacity="0.9" stroke-width="1" shape-rendering="crispEdges" stroke-dasharray="none" style="shape-rendering: crispedges; cursor: default;" opacity="1"></rect>

    This is how it looks -

    image

    help wanted 
    opened by jeetendra-choudhary 2
  • Map collections are not auto download

    Map collections are not auto download

    Need to implement MAP chart using fusion charts library but some how with npm package installer I can not able to download all map collection. rather I have to download those files from your official website and then need to paste in map folder.

    I tried 4-5 times but maps are not downloaded along with npm package.

    Do we have any other way to handle this issue?

    opened by ankitkanojia 2
  • Possible import correction

    Possible import correction

    Very new to react but I think it should be import ReactFC from 'react-fusioncharts' in the documentation instead of import react-fusioncharts from 'react-fusioncharts'. I might be using the modules wrong though.

    Used with wepack

    opened by myersr 2
  • How to enable scrolling on mobile view, when the initial touch is over the chart area ?

    How to enable scrolling on mobile view, when the initial touch is over the chart area ?

    I'm using the ReactFC component to build cross platform dashboard application with React and CapacitorJS. When we are in mobile view, the scroll is not working if the initial touch is inside the chart area, which causes bad UX (the user needs to search an area which outside chart boundaries to be able to scroll down to the next charts). Is there any option to change this behavior ?

    I'm using licensed 3.1.2 react-fusioncharts version

    opened by dejan92 0
  • can we create  chart of  Combination of React Bar, Line and Area Charts

    can we create chart of Combination of React Bar, Line and Area Charts

    Hi , Is it possible to create chart which is combination of bar , line chart ? i tried <ReactFusioncharts type="mscombi2d" width="100%" height="100%" dataFormat="JSON" dataSource={dataSource} /> which shows column where as i need Bar .. is it possible to do it ?

    opened by ramya298 3
  • Incorrect urls for your example data

    Incorrect urls for your example data

    Should probably point to:

    • https://raw.githubusercontent.com/fusioncharts/dev_centre_docs/master/assets/datasources/fusiontime/examples/online-sales-single-series-area-data-plot/data.json
    • https://raw.githubusercontent.com/fusioncharts/dev_centre_docs/master/assets/datasources/fusiontime/examples/online-sales-single-series-area-data-plot/schema.json
    Screen Shot 2020-10-23 at 2 09 35 PM Screen Shot 2020-10-23 at 2 10 11 PM Screen Shot 2020-10-23 at 2 10 24 PM
    opened by samtes 1
  • Build error with NextJs

    Build error with NextJs

    Hi, I faced some difficulties which I cannot solve, so I am here for help. I would like to use fusioncharts but in the built project the charts do now show up, and the console throws an error: Uncaught SyntaxError: Unexpected token ( .

    I recreated the basics in a new example NextJS app and also had the same problem when I build it, you can check it out: https://github.com/Lunatial/FusionCharts

    Another problem of mine is that (I could only try it in development mode) the fusionCharts tried to download google-fonts by CDN, and I do not know how to disable that effort.

    opened by Lunatial 13
  • Updated new samples

    Updated new samples

    opened by sghosh9 0
Owner
Max Brown
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Max Brown
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