class Bio::Tcoffee::DEFAULT_PARSER

CLUSTAL W result data (*.aln file) parser class.

Constants

DELIMITER: Delimiter of each entry. Bio::FlatFile uses it. In Bio::ClustalW::Report, it it nil (1 entry 1 file).

Attributes

raw [R]

string of whole result

seqclass [R]

sequence class (one of Bio::Sequence, Bio::Sequence::NA, Bio::Sequence::AA, …)

Public Class Methods

new (str, seqclass = nil)

Source

   # File lib/bio/appl/clustalw/report.rb
46 def initialize(str, seqclass = nil)
47   @raw = str
48   @align = nil
49   @match_line = nil
50   @header = nil
51   case seqclass
52   when /PROTEIN/i
53     @seqclass = Bio::Sequence::AA
54   when /[DR]NA/i
55     @seqclass = Bio::Sequence::NA
56   else
57     if seqclass.is_a?(Module) then
58       @seqclass = seqclass
59     else
60       @seqclass = Bio::Sequence
61     end
62   end
63 end

Creates new instance. str should be a CLUSTAL format string. seqclass should on of following:

Class: Bio::Sequence::AA, Bio::Sequence::NA, …
String: ‘PROTEIN’, ‘DNA’, …

Public Instance Methods

align ()

Source

    # File lib/bio/appl/clustalw/report.rb
112 def align
113   warn "Bio::ClustalW#align will be deprecated. Please use \'alignment\'."
114   alignment
115 end

This will be deprecated. Instead, please use alignment.

Gets an multiple alignment. Returns a Bio::Alignment object.

alignment ()

Source

    # File lib/bio/appl/clustalw/report.rb
103 def alignment
104   do_parse() unless @align
105   @align
106 end

Gets an multiple alignment. Returns a Bio::Alignment object.

get_sequence (row)

Source

   # File lib/bio/appl/clustalw/report.rb
84 def get_sequence(row)
85   a = alignment
86   return nil if row < 0 or row >= a.keys.size
87   id  = a.keys[row]
88   seq = a.to_hash[id]
89   s = Bio::Sequence.new(seq.seq)
90   s.definition = id
91   s
92 end

Returns the Bio::Sequence in the matrix at row ‘row’ as Bio::Sequence object. When row is out of range a nil is returned.

Arguments:

(required) row: Integer

Returns: Bio::Sequence

header ()

Source

   # File lib/bio/appl/clustalw/report.rb
74 def header
75   @header or (do_parse or @header)
76 end

Shows first line of the result data, for example, ‘CLUSTAL W (1.82) multiple sequence alignment’. Returns a string.

match_line ()

Source

   # File lib/bio/appl/clustalw/report.rb
97 def match_line
98   @match_line or (do_parse or @match_line)
99 end

Shows “match line” of CLUSTAL’s alignment result, for example, ‘:* :* .* * .::. ** :* . * . ’. Returns a string.

to_a ()

Source

    # File lib/bio/appl/clustalw/report.rb
131 def to_a
132   alignment.to_fastaformat_array
133 end

Compatibility note: Behavior of the method will be changed in the future.

Gets an array of the sequences. Returns an array of Bio::FastaFormat objects.

to_fasta (*arg)

Source

    # File lib/bio/appl/clustalw/report.rb
121 def to_fasta(*arg)
122   warn "Bio::ClustalW::report#to_fasta is deprecated. Please use \'alignment.output_fasta\'"
123   alignment.output_fasta(*arg)
124 end

This will be deprecated. Instead, please use alignment.output_fasta.

Gets an fasta-format string of the sequences. Returns a string.