https://github.com/cmdcolin/region_retriever
A small script to retrieve jbrowse data from a region
https://github.com/cmdcolin/region_retriever
Last synced: 29 days ago
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A small script to retrieve jbrowse data from a region
- Host: GitHub
- URL: https://github.com/cmdcolin/region_retriever
- Owner: cmdcolin
- Created: 2019-07-25T16:03:36.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2019-07-26T21:15:38.000Z (almost 7 years ago)
- Last Synced: 2025-03-04T23:30:50.461Z (over 1 year ago)
- Language: JavaScript
- Size: 3.91 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# jbrowse_region_retriever
A small script to download NCList data from a list of regions
## Setup
Just run
```
npm install
```
Or
```
yarn
```
To install the dependencies
## Usage
Make a file called regions.json like this
regions.json
```
[
{"refName": "chr1", "start": 0, "end": 10000},
{"refName": "chr2", "start": 50000, "end": 60000},
...
]
```
Then run the script like this
sample usage
node index.js /path/to/data/directory regions.json
Where /path/to/data/directory contains a trackList.json
## Example output
```
ExampleFeatures ctgA 999 2000 . Remark:hga
ExampleFeatures ctgA 1658 1984 . f07
ExampleFeatures ctgA 3013 6130 . f06
ExampleFeatures ctgA 4714 5968 . f05
NameTest ctgA 1099 2000 . Gene:hga
NameTest ctgA 1199 1900 . Protein:HGA
NameTest ctgA 1599 3000 . Gene:hgb
NameTest ctgA 1799 2900 . Protein:HGB
Genes ctgA 1049 9000 EDEN EDEN
snps ctgA 999 1000 FakeSNP1 FakeSNP
ReadingFrame ctgA 1049 9000 EDEN.2 EDEN.2
ReadingFrame ctgA 1049 9000 EDEN.1 EDEN.1
ReadingFrame ctgA 1299 9000 EDEN.3 EDEN.3
Clones ctgA 999 20000 b101.2 b101.2
CDS ctgA 9999 11500 . Apple1
EST ctgA 1049 7300 Match3 agt221.5
EST ctgA 1049 3202 Match1 agt830.5
EST ctgA 1149 7200 Match5 agt767.5
EST ctgA 5409 7503 Match2 agt830.3
EST ctgA 7499 8000 Match4 agt221.3
EST ctgA 7999 9000 Match6 agt767.3
ChromHMM ctgA 0 11960 . 15_Quies
malformed_alignments ctgA 5232 5302 . seg04
malformed_alignments ctgA 5799 6101 . seg04
malformed_alignments ctgA 6441 6854 . seg04
malformed_alignments ctgA 6884 7241 . seg03
malformed_alignments ctgA 7105 7211 . seg04
malformed_alignments ctgA 7409 7737 . seg03
malformed_alignments ctgA 7694 8177 . seg04
malformed_alignments ctgA 8054 8080 . seg03
malformed_alignments ctgA 8305 8999 . seg03
malformed_alignments ctgA 8544 8783 . seg04
malformed_alignments ctgA 8868 8935 . seg04
malformed_alignments ctgA 9403 9825 . seg04
```
Description of output
column 1 - trackLabel
column 2 - refName
column 3 - start
column 4 - end
column 5 - feature id or '.' if not exists
column 6 - feature name or '.' if not exists
Can customize the output as needed by editing the script