Class: Bio::ClustalW

Classes and Modules

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 = [])

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

[Source]

# 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()

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

[Source]

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

log()

This method will be deprecated.

Returns last messages of CLUSTAL W execution.

[Source]

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

option()

option is deprecated. Instead, please use options.

[Source]

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

query(seqs)

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.

[Source]

# 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)

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.

[Source]

# 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)

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

[Source]

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

query_by_filename(path, *arg)

Performs alignment of sequences in the file named path.

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

[Source]

# 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)

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

Compatibility Note: 2nd argument is deprecated and ignored.

[Source]

# 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()

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

[Source]

# 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

Methods

Classes and Modules

Attributes

Public Class methods

Public Instance methods