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https://github.com/kojix2/bio-bigwig
Ruby wrapper to libBigWig compatible with pyBigWig
https://github.com/kojix2/bio-bigwig
bigbed bigwig bioinformatics
Last synced: 22 days ago
JSON representation
Ruby wrapper to libBigWig compatible with pyBigWig
- Host: GitHub
- URL: https://github.com/kojix2/bio-bigwig
- Owner: kojix2
- License: mit
- Created: 2021-12-15T06:12:25.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2024-02-10T00:43:43.000Z (9 months ago)
- Last Synced: 2024-04-21T02:15:32.659Z (7 months ago)
- Topics: bigbed, bigwig, bioinformatics
- Language: C
- Homepage:
- Size: 264 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Awesome Lists containing this project
README
# bio-bigwig
[](https://rubygems.org/gems/bio-bigwig)
[](https://github.com/kojix2/bio-bigwig/actions/workflows/ci.yml)
[](https://rubydoc.info/gems/bio-bigwig)
[](https://doi.org/10.5281/zenodo.13860901)
Ruby wrapper to [libBigWig](https://github.com/dpryan79/libBigWig) compatible with [pyBigWig](https://github.com/deeptools/pyBigWig).
* Currently, curl does not seem to work well ((Pull requests welcome)).
* File writing is not implemented.
## Installation
```
gem install bio-bigwig
```
## Usage
[bigWig Track Format](https://genome.ucsc.edu/goldenPath/help/bigWig.html)
```ruby
require "bio/bigwig"
bw = Bio::BigWig.open("test/fixtures/test.bw")
bw.is_bigwig?
bw.chroms
# {"1"=>195471971, "10"=>130694993}
bw.chroms("1")
# 195471971
bw.header
# {
# :version => 4, the version number
# :levels => 1, the number of zoom levels
# :bases_covered => 154, the number of bases described
# :min_val => 0, the minimum value
# :max_val => 2, the maximum value
# :sum_data => 272, the sum of all values
# :sum_squared => 500 the sum of all squared values
# }
bw.stats("1", 0, 3)
# [0.2000000054637591]
bw.stats("1", 0, 3, type: :max)
# [0.30000001192092896]
# types
# mean - the average value (default)
# min - the minimum value
# max - the maximum value
# cov/coverage - the fraction of bases covered
# std - the standard deviation of the values
# dev -
# sum -
bw.stats("1",99, 200, type: :max, nbins: 2)
# [1.399999976158142, 1.5]
bw.stats("1")
# [1.3351851569281683]
bw.values("1", 0, 3)
# [0.10000000149011612, 0.20000000298023224, 0.30000001192092896]
bw.values("1", 0, 4)
# [0.10000000149011612, 0.20000000298023224, 0.30000001192092896, NaN]
bw.intervals("1", 0, 3)
# [[0, 1, 0.10000000149011612], [1, 2, 0.20000000298023224], [2, 3, 0.30000001192092896]]
bw.intervals("1")
# [[0, 1, 0.10000000149011612], [1, 2, 0.20000000298023224], [2, 3, 0.30000001192092896],
# [100, 150, 1.399999976158142], [150, 151, 1.5]]
```
[bigBed Track Format](https://genome.ucsc.edu/goldenPath/help/bigBed.html)
```ruby
require "bio/bigwig"
bb = Bio::BigWig.open("test/fixtures/test.bigBed")
bb.entries("chr1", 10000000, 10020000)
# [[10009333, 10009640, "61035\t130\t-\t0.026\t0.42\t404"],
# [10014007, 10014289, "61047\t136\t-\t0.029\t0.42\t404"],
# [10014373, 10024307, "61048\t630\t-\t5.420\t0.00\t2672399"]]
bb = Bio::BigWig.open("test/fixtures/test.bigBed")
bb.entries("chr1", 10000000, 10020000, with_string: false)
# [[10009333, 10009640],
# [10014007, 10014289],
# [10014373, 10024307]]
bb.sql
# table RnaElements
# "BED6 + 3 scores for RNA Elements data "
# (
# string chrom; "Reference sequence chromosome or scaffold"
# uint chromStart; "Start position in chromosome"
# uint chromEnd; "End position in chromosome"
# string name; "Name of item"
# uint score; "Normalized score from 0-1000"
# char[1] strand; "+ or - or . for unknown"
# float level; "Expression level such as RPKM or FPKM. Set to -1 for no data."
# float signif; "Statistical significance such as IDR. Set to -1 for no data."
# uint score2; "Additional measurement/count e.g. number of reads. Set to 0 for no data."
# )
```
## Contributing
Bug reports and pull requests are welcome on GitHub at .
## Development
Pull requests are welcome!
Do you need commit rights to my repository?
Do you want to get admin rights and take over the project?
If so, please feel free to contact us @kojix2.
## License
The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).