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.
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
+ 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
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 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
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
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
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
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
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
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