ruby-igv 0.0.3 → 0.0.6

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@@ -1,7 +1,7 @@
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data/README.md

@@ -1,21 +1,22 @@
-# Ruby-IGV
+# 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).
+[![DOI](https://zenodo.org/badge/281373245.svg)](https://zenodo.org/badge/latestdoi/281373245)
 
 ## Installation
 
+Requirement: [IGV (Integrative Genomics Viewer)](http://software.broadinstitute.org/software/igv/) and [Ruby](https://github.com/ruby/ruby).
+
 ```ruby
 gem install ruby-igv
 ```
 
 ## Usage
 
+[Enable IGV to listen on the port](https://software.broadinstitute.org/software/igv/Preferences#Advanced): Preference > Advanced > Enable port
+
 ```ruby
 igv = IGV.new
 igv.genome 'hg19'
@@ -23,9 +24,13 @@ igv.load   'http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwR
 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
+igv.snapshot_dir = '/tmp/r2/'
+igv.save   'region.jpg'  # save to /tmp/r2/region.png
+igv.send   'echo'        # whatever you want
 ```
 
+See [the list of Batch commands](https://github.com/igvteam/igv/wiki/Batch-commands).
+
 ## Contributing
 
 * [Report bugs](https://github.com/kojix2/ruby-igv/issues)
@@ -33,6 +38,16 @@ igv.send   'echo' #whatever
 * Write, clarify, or fix documentation
 * Suggest or add new features
 
+```
+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 me @kojix2.
+```
+
+## Acknowledgement
+This gem is strongly inspired by a Python script developed by Brent Pedersen.
+* [brentp/bio-playground/igv](https://github.com/brentp/bio-playground).
+
 ## License
 
 The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).

data/lib/igv/version.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 class IGV
-  VERSION = '0.0.3'.freeze
+  VERSION = '0.0.6'
 end

data/lib/igv.rb

@@ -1,15 +1,20 @@
+# frozen_string_literal: true
+
 require 'igv/version'
 require 'socket'
 require 'fileutils'
 
+# The Integrative Genomics Viewer (IGV)
+# https://software.broadinstitute.org/software/igv/
 class IGV
   class Error < StandardError; end
 
-  attr_reader :host, :port, :snapshot_dir, :commands
+  attr_reader :host, :port, :snapshot_dir, :history
+
   def initialize(host: '127.0.0.1', port: 60_151, snapshot_dir: Dir.pwd)
     @host = host
     @port = port
-    @commands = []
+    @history = []
     connect
     set_snapshot_dir(snapshot_dir)
   end
@@ -25,16 +30,25 @@ class IGV
   end
 
   def go(position)
-    send 'goto ' + position
+    send "goto #{position}"
   end
   alias goto go
 
   def genome(name_or_path)
-    send 'genome ' + name_or_path
+    path = File.expand_path(name_or_path)
+    if File.exist?(path)
+      send "genome #{path}"
+    else
+      send "genome #{name_or_path}"
+    end
   end
 
   def load(path_or_url)
-    send 'load ' + path_or_url
+    if URI.parse(path_or_url).scheme
+      send "load #{path_or_url}"
+    else
+      send "load #{File.expand_path(path_or_url)}"
+    end
   end
 
   def region(contig, start, end_)
@@ -42,28 +56,18 @@ class IGV
   end
 
   def sort(option = 'base')
-    if %w[base position strand quality sample readGroup].include? option
-      send 'sort ' + option
-    else
+    unless %w[base position strand quality sample readGroup].include? option
       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
+    send "sort #{option}"
   end
-  alias set_snapshot_dir snapshot_dir=
 
-  def expand(_track = '')
+  def expand(track = '')
     send "expand #{track}"
   end
 
-  def collapse(_track = '')
+  def collapse(track = '')
     send "collapse #{track}"
   end
 
@@ -77,18 +81,28 @@ class IGV
   alias quit exit
 
   def send(cmd)
-    @commands << cmd
+    @history << cmd
     @socket.puts(cmd.encode(Encoding::UTF_8))
     @socket.gets&.chomp("\n")
   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 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)
+      send "snapshot #{File.basename(file_path)}"
     else
       send 'snapshot'
     end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ruby-igv
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.6
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-07-22 00:00:00.000000000 Z
+date: 2022-08-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -66,7 +66,7 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-description: Operate IGV (Integrative Genomics Viewer) from Ruby.
+description: Control IGV (Integrative Genomics Viewer) with Ruby.
 email:
 - 2xijok@gmail.com
 executables: []
@@ -89,15 +89,15 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: 2.3.0
+      version: '2.4'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.2
+rubygems_version: 3.3.7
 signing_key: 
 specification_version: 4
-summary: Operate IGV (Integrative Genomics Viewer) from Ruby.
+summary: Control IGV (Integrative Genomics Viewer) with Ruby.
 test_files: []