ruby-igv 0.0.2

checksums.yaml

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data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2020 kojix2
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README.md

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+# Ruby-IGV
+
+[![Gem Version](https://badge.fury.io/rb/ruby-igv.svg)](https://badge.fury.io/rb/ruby-igv)
+[![Docs Latest](https://img.shields.io/badge/docs-latest-blue.svg)](https://rubydoc.info/gems/ruby-igv)
+[![The MIT License](https://img.shields.io/badge/license-MIT-orange.svg)](LICENSE.txt)
+
+Using [Integrative Genomics Viewer (IGV)](http://software.broadinstitute.org/software/igv/) with the Ruby language.
+
+Based on [brentp/bio-playground/igv](https://github.com/brentp/bio-playground).
+
+## Installation
+
+```ruby
+gem install ruby-igv
+```
+
+## Usage
+
+```ruby
+igv = IGV.new
+igv.genome 'hg19'
+igv.load   'http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562G1AlnRep1.bam'
+igv.go     'chr18:78,016,233-78,016,640'
+igv.save   '/tmp/r/region.svg'
+igv.save   '/tmp/r/region.png'
+igv.send   'echo' #whatever
+```
+
+## Contributing
+
+* [Report bugs](https://github.com/kojix2/ruby-igv/issues)
+* Fix bugs and submit [pull requests](https://github.com/kojix2/ruby-igv/pulls)
+* Write, clarify, or fix documentation
+* Suggest or add new features
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).

data/lib/igv.rb

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+require 'igv/version'
+require 'socket'
+require 'fileutils'
+require 'pathname'
+
+class IGV
+  class Error < StandardError; end
+
+  attr_reader :host, :port, :snapshot_dir, :commands
+  def initialize(host: '127.0.0.1', port: 60_151, snapshot_dir: Dir.pwd)
+    @host = host
+    @port = port
+    @commands = []
+    connect
+    set_snapshot_dir(snapshot_dir)
+  end
+
+  # def self.start
+  # end
+
+  def connect
+    @socket&.close
+    @socket = Socket.new(Socket::AF_INET, Socket::SOCK_STREAM)
+    addr = Socket.sockaddr_in(port, host)
+    @socket.connect(addr)
+  end
+
+  def go(position)
+    send 'goto ' + position
+  end
+  alias goto go
+
+  def genome(name_or_path)
+    send 'genome ' + name_or_path
+  end
+
+  def load(path_or_url)
+    send 'load ' + path_or_url
+  end
+
+  def region(contig, start, end_)
+    send ['region', contig, start, end_].join(' ')
+  end
+
+  def sort(option = 'base')
+    if %w[base position strand quality sample readGroup].include? option
+      send 'sort ' + option
+    else
+      raise 'options is one of: base, position, strand, quality, sample, and readGroup.'
+    end
+  end
+
+  def snapshot_dir=(snapshot_dir)
+    snapshot_dir = File.expand_path(snapshot_dir)
+    return if snapshot_dir == @snaphot_dir
+
+    FileUtils.mkdir_p(snapshot_dir)
+    send "snapshotDirectory #{snapshot_dir}"
+    @snapshot_dir = snapshot_dir
+  end
+  alias set_snapshot_dir snapshot_dir=
+
+  def expand(_track = '')
+    send "expand #{track}"
+  end
+
+  def collapse(_track = '')
+    send "collapse #{track}"
+  end
+
+  def clear
+    send 'clear'
+  end
+
+  def send(cmd)
+    @commands << cmd
+    cmd += "\n"
+    @socket.puts(cmd.encode(Encoding::UTF_8))
+    @socket.readline.chomp("\n")
+  end
+
+  def save(file_path = nil)
+    if file_path
+      # igv assumes the path is just a single filename, but
+      # we can set the snapshot dir. then just use the filename.
+      dir_path = File.dirname(file_path)
+      set_snapshot_dir(File.expand_path(dir_path)) if dir_path != '.'
+      send 'snapshot ' + File.basename(file_path)
+    else
+      send 'snapshot'
+    end
+  end
+  alias snapshot save
+end

data/lib/igv/version.rb

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+class IGV
+  VERSION = '0.0.2'.freeze
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: ruby-igv
+version: !ruby/object:Gem::Version
+  version: 0.0.2
+platform: ruby
+authors:
+- kojix2
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2020-07-21 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: colorize
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: test-unit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Operate IGV (Integrative Genomics Viewer) from Ruby.
+email:
+- 2xijok@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- LICENSE.txt
+- README.md
+- lib/igv.rb
+- lib/igv/version.rb
+homepage: https://github.com/kojix2/ruby-igv
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 2.3.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.1.2
+signing_key: 
+specification_version: 4
+summary: Operate IGV (Integrative Genomics Viewer) from Ruby.
+test_files: []