Class: IGV

Inherits:
Object
  • Object
show all
Defined in:
lib/igv.rb,
lib/igv/version.rb

Overview

The Integrative Genomics Viewer (IGV) software.broadinstitute.org/software/igv/

Defined Under Namespace

Classes: Error

Constant Summary collapse

VERSION = 
'0.0.6'

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(host: '127.0.0.1', port: 60_151, snapshot_dir: Dir.pwd) ⇒ IGV

Returns a new instance of IGV.



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# File 'lib/igv.rb', line 14

def initialize(host: '127.0.0.1', port: 60_151, snapshot_dir: Dir.pwd)
  @host = host
  @port = port
  @history = []
  connect
  set_snapshot_dir(snapshot_dir)
end

Instance Attribute Details

#history ⇒ Object (readonly)

Returns the value of attribute history.



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# File 'lib/igv.rb', line 12

def history
  @history
end

#host ⇒ Object (readonly)

Returns the value of attribute host.



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# File 'lib/igv.rb', line 12

def host
  @host
end

#port ⇒ Object (readonly)

Returns the value of attribute port.



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# File 'lib/igv.rb', line 12

def port
  @port
end

#snapshot_dir ⇒ Object

Returns the value of attribute snapshot_dir.



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# File 'lib/igv.rb', line 12

def snapshot_dir
  @snapshot_dir
end

Instance Method Details

#clear ⇒ Object 



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# File 'lib/igv.rb', line 74

def clear
  send 'clear'
end

#collapse(track = '') ⇒ Object 



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# File 'lib/igv.rb', line 70

def collapse(track = '')
  send "collapse #{track}"
end

#connect ⇒ Object

def self.start end



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# File 'lib/igv.rb', line 25

def connect
  @socket&.close
  @socket = Socket.new(Socket::AF_INET, Socket::SOCK_STREAM)
  addr = Socket.sockaddr_in(port, host)
  @socket.connect(addr)
end

#exit ⇒ Object Also known as: quit 



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# File 'lib/igv.rb', line 78

def exit
  send 'exit'
end

#expand(track = '') ⇒ Object 



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# File 'lib/igv.rb', line 66

def expand(track = '')
  send "expand #{track}"
end

#genome(name_or_path) ⇒ Object 



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# File 'lib/igv.rb', line 37

def 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

#go(position) ⇒ Object Also known as: goto 



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# File 'lib/igv.rb', line 32

def go(position)
  send "goto #{position}"
end

#load(path_or_url) ⇒ Object 



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# File 'lib/igv.rb', line 46

def 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

#region(contig, start, end_) ⇒ Object 



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# File 'lib/igv.rb', line 54

def region(contig, start, end_)
  send ['region', contig, start, end_].join(' ')
end

#save(file_path = nil) ⇒ Object Also known as: snapshot 



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# File 'lib/igv.rb', line 99

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

#send(cmd) ⇒ Object 



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# File 'lib/igv.rb', line 83

def send(cmd)
  @history << cmd
  @socket.puts(cmd.encode(Encoding::UTF_8))
  @socket.gets&.chomp("\n")
end

#sort(option = 'base') ⇒ Object 



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# File 'lib/igv.rb', line 58

def sort(option = 'base')
  unless %w[base position strand quality sample readGroup].include? option
    raise 'options is one of: base, position, strand, quality, sample, and readGroup.'
  end

  send "sort #{option}"
end