ruby-igv 0.0.4 → 0.0.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/README.md +5 -3
- data/lib/igv.rb +14 -9
- data/lib/igv/version.rb +3 -1
- metadata +6 -6
checksums.yaml
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: a162dd0aa5d26fd45b3da87eb9c8e4faec6bc47f6922dc850dc5f5f556405c26
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data.tar.gz: 6ceb747c0f8b5b697f561c2836c8e021d29fd2bcc0cc5bc91cc7916bc24b0c61
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metadata.gz:
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metadata.gz: 0e05cd137522d371629790616283c5f2c31f96f9882979d64f46ab83530ccf14569bc039213ddda103653ad009d9818e50f1e95e5f3738cb985903da6d8c6ed2
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data.tar.gz: 361d5f9e770f4f78304e4b99672e6e5e2c116bd8994b5d57076b808b40b27ae5fa493c74842923d4165adef2b79827ae85e5d711d9ce279f001afddb0676df95
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data/README.md
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[](https://rubydoc.info/gems/ruby-igv)
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[](LICENSE.txt)
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Based on [brentp/bio-playground/igv](https://github.com/brentp/bio-playground).
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Controlling [Integrative Genomics Viewer (IGV)](http://software.broadinstitute.org/software/igv/) with the [Ruby](https://github.com/ruby/ruby) language.
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## Installation
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@@ -37,6 +35,10 @@ igv.send 'echo' # whatever you want
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* Write, clarify, or fix documentation
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* Suggest or add new features
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# Acknowledgement
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This gem is strongly inspired by a Python script developed by Brent Pedersen.
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* [brentp/bio-playground/igv](https://github.com/brentp/bio-playground).
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## License
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The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
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data/lib/igv.rb
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# frozen_string_literal: true
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require 'igv/version'
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require 'socket'
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require 'fileutils'
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# The Integrative Genomics Viewer (IGV)
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# https://software.broadinstitute.org/software/igv/
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class IGV
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class Error < StandardError; end
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attr_reader :host, :port, :snapshot_dir, :history
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def initialize(host: '127.0.0.1', port: 60_151, snapshot_dir: Dir.pwd)
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@host = host
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@port = port
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end
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def go(position)
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send
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send "goto #{position}"
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end
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alias goto go
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def genome(name_or_path)
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path = File.expand_path(name_or_path)
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if File.exist?(path)
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send
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send "genome #{path}"
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else
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send
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send "genome #{name_or_path}"
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end
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end
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def load(path_or_url)
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if URI.parse(path_or_url).scheme
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send
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send "load #{path_or_url}"
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else
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send
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send "load #{File.expand_path(path_or_url)}"
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end
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end
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end
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def sort(option = 'base')
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send 'sort ' + option
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else
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unless %w[base position strand quality sample readGroup].include? option
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raise 'options is one of: base, position, strand, quality, sample, and readGroup.'
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end
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send "sort #{option}"
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end
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def expand(_track = '')
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# we can set the snapshot dir. then just use the filename.
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dir_path = File.dirname(file_path)
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set_snapshot_dir(File.expand_path(dir_path)) if dir_path != '.'
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send
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send "snapshot #{File.basename(file_path)}"
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else
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send 'snapshot'
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end
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data/lib/igv/version.rb
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metadata
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--- !ruby/object:Gem::Specification
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name: ruby-igv
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version: !ruby/object:Gem::Version
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version: 0.0.
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version: 0.0.5
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platform: ruby
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authors:
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- kojix2
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2020-
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date: 2020-12-10 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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description:
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description: Control IGV (Integrative Genomics Viewer) with Ruby.
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email:
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- 2xijok@gmail.com
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executables: []
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requirements:
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- !ruby/object:Gem::Version
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version: 2.
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version: '2.4'
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required_rubygems_version: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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rubygems_version: 3.1.
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rubygems_version: 3.1.4
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signing_key:
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specification_version: 4
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summary:
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summary: Control IGV (Integrative Genomics Viewer) with Ruby.
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test_files: []
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