class Bio::ClustalW

Bio::ClustalW is a CLUSTAL W execution wrapper class. Its object is also called an alignment factory. CLUSTAL W is a very popular software for multiple sequence alignment.

Attributes

command[R]

Returns last command-line strings executed by this factory. Note that filenames described in the command-line may already be removed because they are temporary files. Returns an array.

data_stdout[RW]

Last output to the stdout.

exit_status[R]

Last exit status

options[RW]

options

output[R]

Returns last raw alignment result (String or nil).

output_dnd[R]

Returns last alignment guild-tree (file.dnd).

program[RW]

name of the program (usually 'clustalw' in UNIX)

report[R]

Returns last alignment result. Returns a Bio::ClustalW::Report object.

Public Class Methods

new(program = 'clustalw', opt = []) click to toggle source

Creates a new CLUSTAL W execution wrapper object (alignment factory).

# File lib/bio/appl/clustalw.rb, line 41
def initialize(program = 'clustalw', opt = [])
  @program = program
  @options = opt
  @command = nil
  @output = nil
  @report = nil
  @data_stdout = nil
  @exit_status = nil
  @output_dnd = nil
end

Public Instance Methods

errorlog() click to toggle source

+ errorlog is deprecated (no replacement) and returns empty string.

# File lib/bio/appl/clustalw.rb, line 196
def errorlog
  warn "errorlog is deprecated (no replacement) and returns empty string."
  ''
end

log() click to toggle source

This method will be deprecated.

Returns last messages of CLUSTAL W execution.

# File lib/bio/appl/clustalw.rb, line 73
def log
  #warn 'Bio::ClustalW#log will be deprecated.'
  @data_stdout
end

option() click to toggle source

option is deprecated. Instead, please use options.

# File lib/bio/appl/clustalw.rb, line 59
def option
  warn "Bio::ClustalW#option is deprecated. Please use options."
  options
end

query(seqs) click to toggle source

Executes the program(clustalw). If seqs is not nil, perform alignment for seqs. If seqs is nil, simply executes CLUSTAL W.

Compatibility note: When seqs is nil, returns true if the program exits normally, and returns false if the program exits abnormally.

# File lib/bio/appl/clustalw.rb, line 108
def query(seqs)
  if seqs then
    query_align(seqs)
  else
    exec_local(@options)
    @exit_status.exitstatus == 0 ? true : false
  end
end

query_align(seqs) click to toggle source

Note that this method will be renamed to query_alignment.

Performs alignment for seqs. seqs should be Bio::Alignment or Array of sequences or nil.

Compatibility Note: Nucleic or amino is not determined by this method.

# File lib/bio/appl/clustalw.rb, line 123
def query_align(seqs)
  unless seqs.is_a?(Bio::Alignment)
    seqs = Bio::Alignment.new(seqs)
  end
  query_string(seqs.output_fasta(:width => 70,
                                 :avoid_same_name => true))
end

query_alignment(seqs) click to toggle source

Performs alignment for seqs. seqs should be Bio::Alignment or Array of sequences or nil.

# File lib/bio/appl/clustalw.rb, line 133
def query_alignment(seqs)
  query_align(seqs)
end

query_by_filename(path, *arg) click to toggle source

Performs alignment of sequences in the file named path.

Compatibility Note: 2nd argument (seqtype) is deprecated and ignored.

# File lib/bio/appl/clustalw.rb, line 159
def query_by_filename(path, *arg)
  if arg.size > 0 then
    warn '2nd argument of Bio::ClustalW#query_by_filename is ignored'
  end

  tf_out = Tempfile.open('clustalout')
  tf_out.close(false)
  tf_dnd = Tempfile.open('clustaldnd')
  tf_dnd.close(false)

  opt = [ "-align",
    "-infile=#{path}",
    "-outfile=#{tf_out.path}",
    "-newtree=#{tf_dnd.path}",
    "-outorder=input"
  ]
  #opt << "-type=#{seqtype}" if seqtype
  opt.concat(@options)
  exec_local(opt)
  tf_out.open
  @output = tf_out.read
  tf_out.close(true)
  tf_dnd.open
  @output_dnd = tf_dnd.read
  tf_dnd.close(true)
  @report = Report.new(@output)
  @report
end

query_string(str, *arg) click to toggle source

Performs alignment for str. str should be a string that can be recognized by CLUSTAL W.

Compatibility Note: 2nd argument is deprecated and ignored.

# File lib/bio/appl/clustalw.rb, line 141
def query_string(str, *arg)
  if arg.size > 0 then
    warn '2nd argument of Bio::ClustalW#query_string is ignored'
  end
  begin
    tf_in = Tempfile.open('align')
    tf_in.print str
  ensure
    tf_in.close(false)
  end
  r = query_by_filename(tf_in.path)
  tf_in.close(true)
  r
end

reset() click to toggle source

Clear the internal data and status, except program and options.

# File lib/bio/appl/clustalw.rb, line 92
def reset
  @command = nil
  @output = nil
  @report = nil
  @exit_status = nil
  @data_stdout = nil
  @output_dnd = nil
end