Class: IGV

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

Overview

The Integrative Genomics Viewer (IGV) Ruby client. Provides a Ruby interface to control IGV via its batch command protocol.

See Also:

Defined Under Namespace

Classes: Error

Constant Summary collapse

VERSION = 
'0.0.10'

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

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

Create IGV client object.

Parameters:

  • host (String) (defaults to: '127.0.0.1') —

    Hostname or IP address of IGV server.

  • port (Integer) (defaults to: 60_151) —

    Port number of IGV server.

  • snapshot_dir (String) (defaults to: Dir.pwd) —

    Directory path to save snapshots.

Raises:

  • (ArgumentError) 


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# File 'lib/igv.rb', line 23

def initialize(host: '127.0.0.1', port: 60_151, snapshot_dir: Dir.pwd)
  raise ArgumentError, 'IGV#initialize does not accept a block.' if block_given?

  @host = host
  @port = port
  @snapshot_dir = File.expand_path(snapshot_dir)
  @history = []
end

Instance Attribute Details

#history ⇒ Object (readonly)

Returns the value of attribute history.



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# File 'lib/igv.rb', line 15

def history
  @history
end

#host ⇒ Object (readonly)

Returns the value of attribute host.



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# File 'lib/igv.rb', line 15

def host
  @host
end

#port ⇒ Object (readonly)

Returns the value of attribute port.



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# File 'lib/igv.rb', line 15

def port
  @port
end

Class Method Details

.open(host: '127.0.0.1', port: 60_151, snapshot_dir: Dir.pwd) {|IGV| ... } ⇒ IGV

Create IGV object and connect to IGV server. This method accepts a block.

Parameters:

  • host (String) (defaults to: '127.0.0.1') —

    Hostname or IP address of IGV server.

  • port (Integer) (defaults to: 60_151) —

    Port number of IGV server.

  • snapshot_dir (String) (defaults to: Dir.pwd) —

    Directory path to save snapshots.

Yields:

  • (IGV) —

    IGV client object.

Returns:

  • (IGV) —

    IGV client object.



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# File 'lib/igv.rb', line 40

def self.open(host: '127.0.0.1', port: 60_151, snapshot_dir: Dir.pwd)
  igv = new(host: host, port: port, snapshot_dir: snapshot_dir)
  igv.connect
  return igv unless block_given?

  begin
    yield igv
  ensure
    @socket&.close
  end
  igv
end

.start(port: 60_151, command: 'igv', snapshot_dir: Dir.pwd) ⇒ IGV

Note:

This will spawn a new IGV process and connect to it.

Launch IGV from Ruby script.

Parameters:

  • port (Integer) (defaults to: 60_151) —

    Port number.

  • command (String) (defaults to: 'igv') —

    Command to launch IGV.

  • snapshot_dir (String) (defaults to: Dir.pwd) —

    Directory path to save snapshots.

Returns:

  • (IGV) —

    IGV client object.



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# File 'lib/igv.rb', line 68

def self.start(port: 60_151, command: 'igv', snapshot_dir: Dir.pwd)
  case port_open?(port)
  when nil   then warn "[ruby-igv] Cannot tell if port #{port} is open"
  when true  then raise("Port #{port} is already in use")
  when false then warn "[ruby-igv] Port #{port} is available"
  else raise "Unexpected return value from port_open?(#{port})"
  end
  r, w = IO.pipe
  pid_igv = spawn(command, '-p', port.to_s, pgroup: true, out: w, err: w)
  pgid_igv = Process.getpgid(pid_igv)
  Process.detach(pid_igv)
  puts "\e[33m"
  while (line = r.gets.chomp("\n"))
    puts line
    break if line.include? "Listening on port #{port}"
  end
  puts "\e[0m"
  igv = self.open(port: port, snapshot_dir: snapshot_dir)
  igv.instance_variable_set(:@pgid_igv, pgid_igv)
  igv
end

Instance Method Details

#clear ⇒ self

Note:

IGV Batch command: clear

Clear all loaded tracks and data.

Examples:

igv.clear

Returns:

  • (self) —

    Returns self for method chaining.



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# File 'lib/igv.rb', line 329

def clear
  send :clear
  self
end

#clear_access_tokens ⇒ String

Note:

IGV Batch command: clearAccessTokens

Clears all access tokens.

Examples:

igv.clear_access_tokens

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 630

def clear_access_tokens
  send :clearAccessTokens
end

#close ⇒ nil

Close the socket. This does not exit IGV.

Returns:

  • (nil) —

    Closes the socket and returns nil.



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# File 'lib/igv.rb', line 121

def close
  @socket&.close
  nil
end

#closed? ⇒ Boolean

Check if the socket is closed.

Returns:

  • (Boolean) 


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# File 'lib/igv.rb', line 128

def closed?
  return true if @socket.nil?

  @socket.closed?
end

#collapse(track = nil) ⇒ String

Note:

IGV Batch command: collapse

Collapse a given track. If not specified, collapses all tracks.

Examples:

igv.collapse
igv.collapse("track1")

Parameters:

  • track (String, nil) (defaults to: nil) —

    Track name (optional).

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 284

def collapse(track = nil)
  send :collapse, track
end

#color_by(option, tag) ⇒ String

Note:

IGV Batch command: colorBy

Set the “color by” option for alignment tracks.

Examples:

igv.color_by("SAMPLE")
igv.color_by("TAG", "NM")

Parameters:

  • option (String) —

    Color by option (e.g. “SAMPLE”, “READ_GROUP”, “TAG”, …).

  • tag (String, nil) —

    Tag name (required for option “TAG”).

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 562

def color_by(option, tag)
  send :colorBy, option, tag
end

#commands ⇒ Object

Open IGV batch command documentation in the browser.



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# File 'lib/igv.rb', line 171

def commands
  require 'launchy'
  Launchy.open('https://igv.org/doc/desktop/#UserGuide/tools/batch/#script-commands')
end

#connect(host2 = @host, port2 = @port, connect_timeout: nil) ⇒ self

Connect to IGV server.

Parameters:

  • host2 (String) (defaults to: @host) —

    Hostname or IP address.

  • port2 (Integer) (defaults to: @port) —

    Port number.

  • connect_timeout (Integer, nil) (defaults to: nil) —

    Timeout in seconds.

Returns:

  • (self) —

    Returns self for method chaining.



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# File 'lib/igv.rb', line 113

def connect(host2 = @host, port2 = @port, connect_timeout: nil)
  @socket&.close
  @socket = Socket.tcp(host2, port2, connect_timeout: connect_timeout)
  self
end

#echo(param = nil) ⇒ String

Note:

IGV Batch command: echo

Write the value of “param” back to the response.

Examples:

igv.echo("Hello!") #=> "Hello!"

Parameters:

  • param (String, nil) (defaults to: nil) —

    The parameter to echo.

Returns:

  • (String) —

    The value of “param”. If param is not specified, “echo”.



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# File 'lib/igv.rb', line 183

def echo(param = nil)
  send :echo, param
end

#exit ⇒ nil Also known as: quit

Note:

IGV Batch command: exit

Exit (close) the IGV application and close the socket.

Examples:

igv.exit

Returns:

  • (nil) —

    Exits IGV and closes the socket.



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# File 'lib/igv.rb', line 340

def exit
  send :exit
  @socket.close
  nil
end

#expand(track = nil) ⇒ String

Note:

IGV Batch command: expand

Expand a given track. If not specified, expands all tracks.

Examples:

igv.expand
igv.expand("track1")

Parameters:

  • track (String, nil) (defaults to: nil) —

    Track name (optional).

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 272

def expand(track = nil)
  send :expand, track
end

#genome(name_or_path) ⇒ String

Note:

IGV Batch command: genome

Select a genome by id, or load a genome (or indexed fasta) from the supplied path.

Examples:

igv.genome("hg19")
igv.genome("/path/to/genome.fa")

Parameters:

  • name_or_path (String) —

    Genome id (e.g. “hg19”) or path to fasta/indexed genome.

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 195

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

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

Note:

IGV Batch command: goto

Go to the specified location or list of loci.

Examples:

igv.goto("chr1:1000-2000")

Parameters:

  • position (String) —

    Locus or list of loci (e.g. “chr1:1000-2000”).

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 232

def goto(position)
  send :goto, position
end

#group(option, tag) ⇒ String

Note:

IGV Batch command: group

Group alignments by the specified option.

Examples:

igv.group("SAMPLE")
igv.group("TAG", "NM")

Parameters:

  • option (String) —

    Group option (e.g. “SAMPLE”, “READ_GROUP”, “TAG”, …).

  • tag (String, nil) —

    Tag name or position (required for option “TAG”).

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 575

def group(option, tag)
  send :group, option, tag
end

#kill ⇒ nil

Note:

Only works for IGV processes started by IGV.start.

Kill IGV process by process group id.

Returns:

  • (nil) —

    Kills the IGV process if started by this client, otherwise does nothing.



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# File 'lib/igv.rb', line 94

def kill
  if instance_variable_defined?(:@pgid_igv)
    warn '[ruby-igv] This method kills the process with the group ID specified at startup. Please use exit or quit if possible.'
  else
    warn '[ruby-igv] The kill method terminates only IGV commands invoked by the start method. Otherwise, use exit or quit.'
    return nil
  end
  pgid = @pgid_igv
  Process.kill(:TERM, -pgid)
  close
  nil
end

#load(path_or_url, index: nil) ⇒ String

Note:

IGV Batch command: load

Load a data or session file by specifying a full path to a local file or a URL.

Examples:

igv.load("http://example.com/data.bam")
igv.load("/path/to/data.bam", index: "/path/to/data.bai")

Parameters:

  • path_or_url (String) —

    Path to a local file or a URL.

  • index (String, nil) (defaults to: nil) —

    Optional index file path.

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 213

def load(path_or_url, index: nil)
  path_or_url = if URI.parse(path_or_url).scheme
                  path_or_url
                else
                  File.expand_path(path_or_url)
                end
  index = "index=#{index}" if index
  send :load, path_or_url, index
rescue URI::InvalidURIError
  raise ArgumentError, "Invalid URI or file path: #{path_or_url}"
end

#max_panel_height(height) ⇒ String

Note:

IGV Batch command: maxPanelHeight

Set the number of vertical pixels (height) of each panel to include in image.

Examples:

igv.max_panel_height(2000)

Parameters:

  • height (Integer) —

    Height in pixels.

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 549

def max_panel_height(height)
  send :maxPanelHeight, height
end

#new ⇒ self

Note:

IGV Batch command: new

Create a new session. Unloads all tracks except the default genome annotations.

Examples:

igv.new

Returns:

  • (self) —

    Returns self for method chaining.



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# File 'lib/igv.rb', line 318

def new
  send :new
  self
end

#overlay(overlaid_track, *tracks) ⇒ String

Note:

IGV Batch command: overlay

Overlay a list of tracks.

Examples:

igv.overlay("track1", "track2", "track3")

Parameters:

  • overlaid_track (String) —

    The track to overlay.

  • tracks (Array<String>) —

    List of tracks to overlay.

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 587

def overlay(overlaid_track, *tracks)
  send :overlay, overlaid_track, *tracks
end

#preferences(key, value) ⇒ String

Note:

IGV Batch command: preference

Temporarily set the preference named key to the specified value.

Examples:

igv.preferences("SAM.READ_GROUP_COLOR", "sample")

Parameters:

  • key (String) —

    Preference key.

  • value (String) —

    Preference value.

Returns:

  • (String) —

    IGV response.

See Also:



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# File 'lib/igv.rb', line 423

def preferences(key, value)
  send :preferences, key, value
end

#region(chr, start, end_) ⇒ String

Note:

IGV Batch command: region

Define a region of interest bounded by the two loci.

Examples:

igv.region("chr1", 100, 200)

Parameters:

  • chr (String) —

    Chromosome name.

  • start (Integer) —

    Start position.

  • end_ (Integer) —

    End position.

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 246

def region(chr, start, end_)
  send :region, chr, start, end_
end

#save_session(file_path) ⇒ String

Note:

IGV Batch command: saveSession

Save the current session.

Examples:

igv.save_session("session.xml")

Parameters:

  • file_path (String) —

    Path to the session file.

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 440

def save_session(file_path)
  file_path = File.expand_path(file_path)
  send :saveSession, file_path
end

#scroll_to_top ⇒ String

Note:

IGV Batch command: scrollToTop

Scroll all panels to the top of the view.

Examples:

igv.scroll_to_top

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 597

def scroll_to_top
  send :scrollToTop
end

#send(*cmds) ⇒ String

Send batch commands to IGV.

Examples:

igv.send("goto", "chr1:1000-2000")

Parameters:

  • cmds (Array<String, Symbol, Numeric>) —

    Batch commands.

Returns:

  • (String) —

    Response from IGV.



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# File 'lib/igv.rb', line 140

def send(*cmds)
  cmd = \
    cmds
    .compact
    .map do |cm|
      case cm
      when String, Symbol, Numeric          then cm.to_s
      when ->(c) { c.respond_to?(:to_str) } then cm.to_str
      else raise ArgumentError, "#{cm.inspect} is not a string"
      end.strip.encode(Encoding::UTF_8)
    end
    .join(' ')
  @history << cmd
  @socket.puts(cmd)
  @socket.gets&.chomp("\n")
end

#separate(overlaid_track_name) ⇒ String

Note:

IGV Batch command: separate

Separate an overlaid track into its constituitive tracks.

Examples:

igv.separate("track1")

Parameters:

  • overlaid_track_name (String) —

    The name of the overlaid track to separate.

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 608

def separate(overlaid_track_name)
  send :separate, overlaid_track_name
end

#set(cmd, *params) ⇒ String

Syntactic sugar for IGV commands that begin with set.

Examples:

igv.set :SleepInterval, 100
igv.send "setSleepInterval", 100 # same as above

Parameters:

  • cmd (String, Symbol) —

    Batch command name (without “set” prefix).

  • params (Array<String, Symbol, Numeric>) —

    Parameters for the command.

Returns:

  • (String) —

    Response from IGV.



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# File 'lib/igv.rb', line 165

def set(cmd, *params)
  cmd = "set#{cmd}"
  send(cmd, *params)
end

#set_access_token(token, host = nil) ⇒ String

Note:

IGV Batch command: setAccessToken

Set an access token to be used in an Authorization header for all requests to host.

Examples:

igv.set_access_token("mytoken", "example.com")

Parameters:

  • token (String) —

    The access token.

  • host (String, nil) (defaults to: nil) —

    The host to use the token for (optional).

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 620

def set_access_token(token, host = nil)
  send :setAccessToken, token, host
end

#set_alt_color(color, track) ⇒ String

Note:

IGV Batch command: setAltColor

Set the track “altColor”, used for negative values in a wig track or negative strand features.

Examples:

igv.set_alt_color("255,0,0", "track1")

Parameters:

  • color (String) —

    Color string (e.g. “255,0,0” or “FF0000”).

  • track (String) —

    Track name.

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 453

def set_alt_color(color, track)
  send :setAltColor, color, track
end

#set_color(color, track) ⇒ String

Note:

IGV Batch command: setColor

Set the track color.

Examples:

igv.set_color("FF0000", "track1")

Parameters:

  • color (String) —

    Color string (e.g. “255,0,0” or “FF0000”).

  • track (String) —

    Track name.

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 465

def set_color(color, track)
  send :setColor, color, track
end

#set_data_range(range, track) ⇒ String

Note:

IGV Batch command: setDataRange

Set the data range (scale) for all numeric tracks, or a specific track.

Examples:

igv.set_data_range("0,100", "track1")

Parameters:

  • range (String) —

    Range string (e.g. “0,100” or “auto”).

  • track (String) —

    Track name.

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 477

def set_data_range(range, track)
  send :setDataRange, range, track
end

#set_log_scale(bool, track) ⇒ String

Note:

IGV Batch command: setLogScale

Set the data scale to log (true) or linear (false).

Examples:

igv.set_log_scale(true, "track1")

Parameters:

  • bool (Boolean) —

    true for log scale, false for linear.

  • track (String) —

    Track name (optional).

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 489

def set_log_scale(bool, track)
  bool = 'true' if bool == true
  bool = 'false' if bool == false
  send :setLogScale, bool, track
end

#set_sequence_show_translation(bool) ⇒ String

Note:

IGV Batch command: setSequenceShowTranslation

Show or hide the 3-frame translation rows of the sequence track.

Examples:

igv.set_sequence_show_translation(true)

Parameters:

  • bool (Boolean) —

    true to show, false to hide.

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 513

def set_sequence_show_translation(bool)
  bool = 'true' if bool == true
  bool = 'false' if bool == false
  send :setSequenceShowTranslation, bool
end

#set_sequence_strand(strand) ⇒ String

Note:

IGV Batch command: setSequenceStrand

Set the sequence strand to positive (+) or negative (-).

Examples:

igv.set_sequence_strand("+")

Parameters:

  • strand (String) —

    “+” or “-”.

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 502

def set_sequence_strand(strand)
  send :setSequenceStrand, strand
end

#set_sleep_interval(ms) ⇒ String

Note:

IGV Batch command: setSleepInterval

Set a delay (sleep) time in milliseconds between successive commands.

Examples:

igv.set_sleep_interval(200)

Parameters:

  • ms (Integer) —

    Milliseconds to sleep.

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 526

def set_sleep_interval(ms)
  send :setSleepInterval, ms
end

#set_track_height(height, track) ⇒ String

Note:

IGV Batch command: setTrackHeight

Set the specified track’s height in integer units.

Examples:

igv.set_track_height(50, "track1")

Parameters:

  • height (Integer) —

    Height in pixels.

  • track (String) —

    Track name.

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 538

def set_track_height(height, track)
  send :setTrackHeight, height, track
end

#show_preferences_table ⇒ Object

Show “preference.tab” in your browser.



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# File 'lib/igv.rb', line 428

def show_preferences_table
  require 'launchy'
  Launchy.open('https://raw.githubusercontent.com/igvteam/igv/master/src/main/resources/org/broad/igv/prefs/preferences.tab')
end

#snapshot(file_name = nil) ⇒ Object

Note:

IGV Batch command: snapshot

Save a snapshot of the IGV window to an image file.

Examples:

igv.snapshot("region.png")

Parameters:

  • file_name (String, nil) (defaults to: nil) —

    Name of the image file. If nil, uses the current locus. If filename is omitted, writes a PNG file with a filename generated based on the locus. If filename is specified, the filename extension determines the image file format, which must be either .png or .svg. Passing a path might work, but is not recommended.



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# File 'lib/igv.rb', line 382

def snapshot(file_name = nil)
  return send(:snapshot) if file_name.nil?
  dir_path = File.dirname(file_name)

  # file_name is a file name
  return send(:snapshot, file_name) if dir_path == "."

  # file_name is a path
  file_path = file_name
  warn "[ruby-igv] snapshot: Passing a path is not recommended. "

  if File.absolute_path?(file_path)
    dir_path = File.expand_path(dir_path)
  else
    dir_path = File.expand_path(File.join(@snapshot_dir, dir_path))
  end

  filename = File.basename(file_path)
  
  # Only change directory if needed
  if dir_path == @snapshot_dir
    send(:snapshot, filename)
  else
    # Temporarily change snapshot directory
    original_dir = @snapshot_dir
    snapshot_dir_internal(dir_path)
    result = send(:snapshot, filename)
    snapshot_dir_internal(original_dir)
    result
  end
end

#snapshot_dir(dir_path = nil) ⇒ String

Note:

IGV Batch command: snapshotDirectory

Set or get the directory in which to write images (snapshots).

Examples:

igv.snapshot_dir("/tmp/snapshots")
igv.snapshot_dir #=> "/tmp/snapshots"

Parameters:

  • dir_path (String, nil) (defaults to: nil) —

    Directory path. If nil, returns current snapshot directory.

Returns:

  • (String) —

    IGV response or current directory.



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# File 'lib/igv.rb', line 355

def snapshot_dir(dir_path = nil)
  return @snapshot_dir if dir_path.nil?

  dir_path = File.expand_path(dir_path)
  return if dir_path == @snapshot_dir

  r = snapshot_dir_internal(dir_path)
  @snapshot_dir = dir_path
  r
end

#sort(option = 'base') ⇒ String

Note:

IGV Batch command: sort

Sort alignment or segmented copy number tracks.

Examples:

igv.sort("position")

Parameters:

  • option (String) (defaults to: 'base') —

    Sort option (e.g. “base”, “position”, “strand”, “quality”, “sample”, “readGroup”).

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 257

def sort(option = 'base')
  vop = %w[base position strand quality sample readGroup]
  raise "options is one of: #{vop.join(', ')}" unless vop.include? option

  send :sort, option
end

#squish(track = nil) ⇒ String

Note:

IGV Batch command: squish

Squish a given track. If not specified, squishes all annotation tracks.

Examples:

igv.squish
igv.squish("track1")

Parameters:

  • track (String, nil) (defaults to: nil) —

    Track name (optional).

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 296

def squish(track = nil)
  send :squish, track
end

#viewaspairs(track = nil) ⇒ String

Note:

IGV Batch command: viewaspairs

Set the display mode for an alignment track to “View as pairs”.

Examples:

igv.viewaspairs
igv.viewaspairs("track1")

Parameters:

  • track (String, nil) (defaults to: nil) —

    Track name (optional).

Returns:

  • (String) —

    IGV response.



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# File 'lib/igv.rb', line 308

def viewaspairs(track = nil)
  send :viewaspairs, track
end