Class: Bio::MAFFT

Inherits:

Object

• Object
• Bio::MAFFT

show all

Defined in:

lib/bio/appl/mafft.rb,
lib/bio/appl/mafft/report.rb

Overview

Defined Under Namespace

Classes: Report

Instance Attribute Summary (collapse)

• - (Object) command readonly

  Shows last command-line string.

• - (Object) data_stdout

  Last output to the stdout.

• - (Object) exit_status readonly

  Last exit status.

• - (Object) options

  options.

• - (Object) output readonly

  Shows latest raw alignment result.

• - (Object) program

  program name (usually 'mafft' in UNIX).

• - (Object) report readonly

  Shows last alignment result (instance of Bio::MAFFT::Report class) performed by the factory.

Class Method Summary (collapse)

• + (Object) fftns(n = nil)

  Creates a new alignment factory.

• + (Object) fftnsi

  Creates a new alignment factory.

• + (Object) new2(dir, prog, *opt)

  Creates a new alignment factory.

• + (Object) nwap(n = nil)

  Creates a new alignment factory.

• + (Object) nwns(n = nil, ap = nil)

  Creates a new alignment factory.

• + (Object) nwnsi(all_positive = nil)

  Creates a new alignment factory.

Instance Method Summary (collapse)

• - (MAFFT) initialize(program = 'mafft', opt = []) constructor

  Creates a new alignment factory.

• - (Object) log

  log is deprecated (no replacement) and returns empty string.

• - (Object) option

  option is deprecated.

• - (Object) query(seqs)

  Executes the program.

• - (Object) query_align(seqs, *arg)

  Note that this method will be renamed to query_alignment.

• - (Object) query_alignment(seqs)

  Performs alignment for seqs.

• - (Object) query_by_filename(fn, *arg)

  Performs alignment of sequences in the file named fn.

• - (Object) query_string(str, *arg)

  Performs alignment for str.

• - (Object) reset

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

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# File 'lib/bio/appl/mafft.rb', line 108

def initialize(program = 'mafft', opt = [])
  @program = program
  @options = opt
  @command = nil
  @output = nil
  @report = nil
  @data_stdout = nil
  @exit_status = nil
end

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# File 'lib/bio/appl/mafft.rb', line 133

def command
  @command
end

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# File 'lib/bio/appl/mafft.rb', line 161

def data_stdout
  @data_stdout
end

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# File 'lib/bio/appl/mafft.rb', line 158

def exit_status
  @exit_status
end

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# File 'lib/bio/appl/mafft.rb', line 122

def options
  @options
end

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# File 'lib/bio/appl/mafft.rb', line 151

def output
  @output
end

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# File 'lib/bio/appl/mafft.rb', line 119

def program
  @program
end

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# File 'lib/bio/appl/mafft.rb', line 155

def report
  @report
end

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# File 'lib/bio/appl/mafft.rb', line 47

def self.fftns(n = nil)
  opt = []
  if n.to_s == 'i' then
    self.new2(nil, 'fftnsi', *opt)
  else
    opt << n.to_s if n
    self.new2(nil, 'fftns', *opt)
  end
end

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# File 'lib/bio/appl/mafft.rb', line 59

def self.fftnsi
  self.new2(nil, 'fftnsi')
end

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# File 'lib/bio/appl/mafft.rb', line 98

def self.new2(dir, prog, *opt)
  if dir then
    prog = File.join(dir, prog)
  end
  self.new(prog, opt)
end

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# File 'lib/bio/appl/mafft.rb', line 90

def self.nwap(n = nil)
  self.nwns(n, true)
end

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# File 'lib/bio/appl/mafft.rb', line 67

def self.nwns(n = nil, ap = nil)
  opt = []
  opt << '--all-positive' if ap
  if n.to_s == 'i' then
    self.new2(nil, 'nwnsi', *opt)
  else
    opt << n.to_s if n
    self.new2(nil, 'nwns', *opt)
  end
end

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# File 'lib/bio/appl/mafft.rb', line 81

def self.nwnsi(all_positive = nil)
  opt = []
  opt << '--all-positive' if all_positive
  self.new2(nil, 'nwnsi', *opt)
end

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# File 'lib/bio/appl/mafft.rb', line 141

def log
  warn "Bio::MAFFT#log is deprecated (no replacement) and returns empty string."
  ''
end

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# File 'lib/bio/appl/mafft.rb', line 125

def option
  warn "Bio::MAFFT#option is deprecated. Please use options."
  options
end

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# File 'lib/bio/appl/mafft.rb', line 179

def query(seqs)
  if seqs then
    query_align(seqs)
  else
    exec_local(@options)
    @exit_status.exitstatus == 0 ? true : false
  end
end

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# File 'lib/bio/appl/mafft.rb', line 194

def query_align(seqs, *arg)
  if arg.size > 0 then
    warn '2nd and other arguments of Bio::MAFFT#query_align is ignored'
  end
  unless seqs.is_a?(Bio::Alignment)
    seqs = Bio::Alignment.new(seqs)
  end
  query_string(seqs.output_fasta(:width => 70))
end

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# File 'lib/bio/appl/mafft.rb', line 206

def query_alignment(seqs)
  query_align(seqs)
end

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# File 'lib/bio/appl/mafft.rb', line 232

def query_by_filename(fn, *arg)
  if arg.size > 0 then
    warn '2nd argument of Bio::MAFFT#query_filename is ignored'
  end
  opt = @options + [ fn ]
  exec_local(opt)
  @report = Report.new(@output)
  @report
end

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# File 'lib/bio/appl/mafft.rb', line 214

def query_string(str, *arg)
  if arg.size > 0 then
    warn '2nd and other arguments of Bio::MAFFT#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, *arg)
  tf_in.close(true)
  r
end

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# File 'lib/bio/appl/mafft.rb', line 164

def reset
  @command = nil
  @output = nil
  @report = nil
  @exit_status = nil
  @data_stdout = nil
end