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https://github.com/alexpreynolds/higlass-bigbed-datafetcher
Provide remote access to remotely-hosted bigBed files to HiGlass client applications
https://github.com/alexpreynolds/higlass-bigbed-datafetcher
Last synced: about 21 hours ago
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Provide remote access to remotely-hosted bigBed files to HiGlass client applications
- Host: GitHub
- URL: https://github.com/alexpreynolds/higlass-bigbed-datafetcher
- Owner: alexpreynolds
- License: mit
- Created: 2024-07-02T17:33:33.000Z (4 months ago)
- Default Branch: main
- Last Pushed: 2024-07-11T05:14:33.000Z (4 months ago)
- Last Synced: 2024-07-11T06:35:43.000Z (4 months ago)
- Language: JavaScript
- Size: 1.42 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# higlass-bigbed-datafetcher
Provide remote access to remotely-hosted bigBed files to HiGlass client applications
## Usage
This enables access to a web-hosted bigBed 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 { BigBedDataFetcher } from "higlass-bigbed-datafetcher";
register (
{
dataFetcher: BigBedDataFetcher,
config: BigBedDataFetcher.config,
},
{
pluginType: "dataFetcher",
}
);
```
Configure the view configuration's `horizontal-transcripts` object with `data` attributes pointing to the web-hosted tabix file:
```
{
"name": "My bigBed elements",
"type": "horizontal-transcripts",
"uid": "my_bigbed_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": "bigbed",
"url": "https://example.com/bigBed/my_elements.bb",
"chromSizesUrl": "https://example.com/bigBed/hg38.chromSizes.gz",
},
}
```
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;
}
```
Placeholders are used to change rendering behavior when fields are missing data.