https://github.com/alexpreynolds/higlass-tabix-datafetcher

Provide remote access to remotely-hosted tabix files to HiGlass client applications
https://github.com/alexpreynolds/higlass-tabix-datafetcher

Last synced: about 22 hours ago
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Provide remote access to remotely-hosted tabix files to HiGlass client applications

• Host: GitHub
• URL: https://github.com/alexpreynolds/higlass-tabix-datafetcher
• Owner: alexpreynolds
• License: mit
• Created: 2024-04-09T05:29:43.000Z (7 months ago)
• Default Branch: main
• Last Pushed: 2024-07-18T05:28:17.000Z (4 months ago)
• Last Synced: 2024-07-18T07:23:01.990Z (4 months ago)
• Language: JavaScript
• Size: 464 KB
• Stars: 2
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# higlass-tabix-datafetcher

Provide remote access to remotely-hosted tabix files to HiGlass client applications

## Usage

This enables access to a web-hosted tabix file for use with the `higlass-transcripts` (https://github.com/higlass/higlass-transcripts) plug-in.

Register the data fetcher in your HiGlass application:

```

import register from "higlass-register";

import { TabixDataFetcher } from "higlass-tabix-datafetcher";

register (

  { 

    dataFetcher: TabixDataFetcher, 

    config: TabixDataFetcher.config,

  },

  { 

    pluginType: "dataFetcher",

  }

);

```

Configure the view configuration's `horizontal-transcripts` object with `data` attributes pointing to the web-hosted tabix file:

```

{

  "name": "My Transcripts",

  "type": "horizontal-transcripts",

  "uid": "my_transcripts_uid",

  "options": {

    "fontSize": 9, // font size for labels and amino acids (if available)

    "fontFamily": "Helvetica",

    "labelFontColor": "#333333",

    "labelBackgroundPlusStrandColor": "#ffffff",

    "labelBackgroundMinusStrandColor": "#ffffff",

    "labelStrokePlusStrandColor": "#999999",

    "labelStrokeMinusStrandColor": "#999999",

    "plusStrandColor": "#bdbfff", // color of coding parts of the exon on the plus strand

    "minusStrandColor": "#fabec2", // color of coding parts of the exon on the negative strand

    "utrColor": "#C0EAAF", // color of untranslated regions of the exons

    "backgroundColor": "#ffffff", // color of track background

    "transcriptHeight": 12, // height of the transcripts

    "transcriptSpacing": 2, // space in between the transcripts

    "name": "Gene transcripts",

    "maxTexts": 50, // Maximum number of labels shown on the screen

    "showToggleTranscriptsButton": true, // If the "Show fewer transcripts"/"Show more transcripts" is shown

    "trackHeightAdjustment": "automatic", // if "automatic", the height of the track is adjusted to the number of visible transcripts.

    "startCollapsed": false, // if true, only one transcript is shown

  },

  "data" : {

    "type": "tabix",

    "url": "https://example.com/tabix/my_transcripts.gz",

    "chromSizesUrl": "https://example.com/tabix/hg38.chromSizes.gz",

  },

}

```

There should be an associated index file hosted at `https://example.com/tabix/my_transcripts.gz.tbi`.

The file `https://example.com/tabix/my_transcripts.gz` is compressed with `bgzip` and indexed with `tabix`. For example:

```

$ gunzip -c my_transcripts.gz | more

chr1	11869	14409	DDX11L1-001	101	+	ENSG00000223972.5	ENST00000456328.2	transcribed_unprocessed_pseudogene	11869,12613,13221	12227,12721,14409	.	.

chr1	12010	13670	DDX11L1-002	90	+	ENSG00000223972.5	ENST00000450305.2	transcribed_unprocessed_pseudogene	12010,12179,12613,12975,13221,13453	12057,12227,12697,13052,13374,13670	.	.

chr1	14404	29570	WASH7P-001	101	-	ENSG00000227232.5	ENST00000488147.1	unprocessed_pseudogene	14404,15005,15796,16607,16858,17233,17606,17915,18268,24738,29534	14501,15038,15947,16765,17055,17368,17742,18061,18366,24891,29570	.	.

chr1	17369	17436	MIR6859-1-001	101	-	ENSG00000278267.1	ENST00000619216.1	miRNA	17369	17436	.	.

chr1	29554	31097	MIR1302-2HG-001	101	+	ENSG00000243485.5	ENST00000473358.1	lncRNA	29554,30564,30976	30039,30667,31097	.	.

...

```

The format of data is currently driven by the `formatTranscriptData` function in `higlass-transcripts`, where transcript metadata are stored in thirteen columns:

```

formatTranscriptData(ts) {

  const strand = ts[5];

  const stopCodonPos = ts[12] === "." ? "." : (strand === "+" ? +ts[12] + 2 : +ts[12] - 1);

  const startCodonPos = ts[11] === "." ? "." : (strand === "+" ? +ts[11] - 1 : +ts[11] + 2);

  const exonStarts = ts[9].split(",").map((x) => +x - 1);

  const exonEnds = ts[10].split(",").map((x) => +x);

  const txStart = +ts[1] - 1;

  const txEnd = +ts[2] - 1;

  const result = {

    transcriptId: this.transcriptId(ts),

    transcriptName: ts[3],

    txStart: txStart,

    txEnd: txEnd,

    strand: strand,

    chromName: ts[0],

    codingType: ts[8],

    exonStarts: exonStarts,

    exonEnds: exonEnds,

    startCodonPos: startCodonPos,

    stopCodonPos: stopCodonPos,

    importance: +ts[4],

  };

  return result;

}

```