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 = [])

Source

   # File lib/bio/appl/clustalw.rb
41 def initialize(program = 'clustalw', opt = [])
42   @program = program
43   @options = opt
44   @command = nil
45   @output = nil
46   @report = nil
47   @data_stdout = nil
48   @exit_status = nil
49   @output_dnd = nil
50 end

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

Public Instance Methods

errorlog ()

Source

    # File lib/bio/appl/clustalw.rb
196 def errorlog
197   warn "errorlog is deprecated (no replacement) and returns empty string."
198   ''
199 end

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

log ()

Source

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

This method will be deprecated.

Returns last messages of CLUSTAL W execution.

option ()

Source

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

option is deprecated. Instead, please use options.

query (seqs)

Source

    # File lib/bio/appl/clustalw.rb
108 def query(seqs)
109   if seqs then
110     query_align(seqs)
111   else
112     exec_local(@options)
113     @exit_status.exitstatus == 0 ? true : false
114   end
115 end

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.

query_align (seqs)

Source

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

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.

query_alignment (seqs)

Source

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

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

query_by_filename (path, *arg)

Source

    # File lib/bio/appl/clustalw.rb
159 def query_by_filename(path, *arg)
160   if arg.size > 0 then
161     warn '2nd argument of Bio::ClustalW#query_by_filename is ignored'
162   end
163 
164   tf_out = Tempfile.open('clustalout')
165   tf_out.close(false)
166   tf_dnd = Tempfile.open('clustaldnd')
167   tf_dnd.close(false)
168 
169   opt = [ "-align",
170     "-infile=#{path}",
171     "-outfile=#{tf_out.path}",
172     "-newtree=#{tf_dnd.path}",
173     "-outorder=input"
174   ]
175   #opt << "-type=#{seqtype}" if seqtype
176   opt.concat(@options)
177   exec_local(opt)
178   tf_out.open
179   @output = tf_out.read
180   tf_out.close(true)
181   tf_dnd.open
182   @output_dnd = tf_dnd.read
183   tf_dnd.close(true)
184   @report = Report.new(@output)
185   @report
186 end

Performs alignment of sequences in the file named path.

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

query_string (str, *arg)

Source

    # File lib/bio/appl/clustalw.rb
141 def query_string(str, *arg)
142   if arg.size > 0 then
143     warn '2nd argument of Bio::ClustalW#query_string is ignored'
144   end
145   begin
146     tf_in = Tempfile.open('align')
147     tf_in.print str
148   ensure
149     tf_in.close(false)
150   end
151   r = query_by_filename(tf_in.path)
152   tf_in.close(true)
153   r
154 end

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

Compatibility Note: 2nd argument is deprecated and ignored.

reset ()

Source

   # File lib/bio/appl/clustalw.rb
92 def reset
93   @command = nil
94   @output = nil
95   @report = nil
96   @exit_status = nil
97   @data_stdout = nil
98   @output_dnd = nil
99 end

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