Class: Bio::Blast::Default::Report

Classes and Modules

Class Bio::Blast::Default::Report::HSP
Class Bio::Blast::Default::Report::Hit
Class Bio::Blast::Default::Report::Iteration

Constants

DELIMITER	=	RS = "\nBLAST"		Delimiter of each entry. Bio::FlatFile uses it.
DELIMITER_OVERRUN	=	5		(Integer) excess read size included in DELIMITER.

Attributes

db_len	[R]	number of letters in database
db_num	[R]	number of sequences in database
eff_space	[R]	effective length of the database
entry_overrun	[R]	piece of next entry. Bio::FlatFile uses it.
expect	[R]	e-value threshold specified when BLAST was executed
gap_extend	[R]	gap extend penalty
gap_open	[R]	gap open penalty
iterations	[R]	(PSI-BLAST) Returns iterations. It returns an array of Bio::Blast::Default::Report::Iteration class. Note that normal blastall result usually contains one iteration.
matrix	[R]	name of the matrix
num_hits	[R]	number of hits. Note that this may differ from `hits.size`.
posted_date	[R]	posted date of the database
sc_match	[R]	match score of the matrix
sc_mismatch	[R]	mismatch score of the matrix

Public Class methods

new(str)

Creates a new Report object from BLAST result text.

[Source]

# File lib/bio/appl/blast/format0.rb, line 53
        def initialize(str)
          str = str.sub(/\A\s+/, '')
          str.sub!(/\n(T?BLAST.*)/m, "\n") # remove trailing entries for sure
          @entry_overrun = $1
          @entry = str
          data = str.split(/(?:^[ \t]*\n)+/)

          format0_split_headers(data)
          @iterations = format0_split_search(data)
          format0_split_stat_params(data)
        end

open(filename, *mode)

Opens file by using Bio::FlatFile.open.

[Source]

# File lib/bio/appl/blast/format0.rb, line 48
        def self.open(filename, *mode)
          Bio::FlatFile.open(self, filename, *mode)
        end

Public Instance methods

converged?()

(PSI-BLAST) Same as iterations.last.converged?. Returns true if the last iteration is converged, otherwise, returns false.

[Source]

# File lib/bio/appl/blast/format0.rb, line 221
        def converged?
          @iterations.last.converged?
        end

db()

Returns the name (filename or title) of the database.

[Source]

# File lib/bio/appl/blast/format0.rb, line 245
        def db
          unless defined?(@db)
            if /Database *\: *(.*)/m =~ @f0database then
              a = $1.split(/^/)
              a.pop if a.size > 1
              @db = a.collect { |x| x.sub(/\s+\z/, '') }.join(' ')
            end
          end #unless
          @db
        end

each()

Alias for each_hit

each_hit() {|x| ...}

Iterates over each hit of the last iteration. Same as iterations.last.each_hit. Yields a Bio::Blast::Default::Report::Hit object. This is very useful in most cases, e.g. for blastall results.

[Source]

# File lib/bio/appl/blast/format0.rb, line 196
        def each_hit
          @iterations.last.each do |x|
            yield x
          end
        end

each_iteration() {|x| ...}

(PSI-BLAST) Iterates over each iteration. Same as iterations.each. Yields a Bio::Blast::Default::Report::Iteration object.

[Source]

# File lib/bio/appl/blast/format0.rb, line 186
        def each_iteration
          @iterations.each do |x|
            yield x
          end
        end

entropy()

Same as iterations.last.entropy.

[Source]

# File lib/bio/appl/blast/format0.rb, line 146
        def entropy;        @iterations.last.entropy;        end

gapped_entropy()

Same as iterations.last.gapped_entropy.

[Source]

# File lib/bio/appl/blast/format0.rb, line 153
        def gapped_entropy; @iterations.last.gapped_entropy; end

gapped_kappa()

Same as iterations.last.gapped_kappa.

[Source]

# File lib/bio/appl/blast/format0.rb, line 149
        def gapped_kappa;   @iterations.last.gapped_kappa;   end

gapped_lambda()

Same as iterations.last.gapped_lambda.

[Source]

# File lib/bio/appl/blast/format0.rb, line 151
        def gapped_lambda;  @iterations.last.gapped_lambda;  end

hits()

Same as iterations.last.hits. Returns the last iteration‘s hits. Returns an array of Bio::Blast::Default::Report::Hit object. This is very useful in most cases, e.g. for blastall results.

[Source]

# File lib/bio/appl/blast/format0.rb, line 207
        def hits
          @iterations.last.hits
        end

kappa()

Same as iterations.last.kappa.

[Source]

# File lib/bio/appl/blast/format0.rb, line 142
        def kappa;          @iterations.last.kappa;          end

lambda()

Same as iterations.last.lambda.

[Source]

# File lib/bio/appl/blast/format0.rb, line 144
        def lambda;         @iterations.last.lambda;         end

message()

(PSI-BLAST) Same as iterations.last.message.

[Source]

# File lib/bio/appl/blast/format0.rb, line 213
        def message
          @iterations.last.message
        end

pattern()

(PHI-BLAST) Same as iterations.first.pattern. Note that it returns the FIRST iteration‘s value.

[Source]

# File lib/bio/appl/blast/format0.rb, line 173
        def pattern; @iterations.first.pattern; end

pattern_positions()

(PHI-BLAST) Same as iterations.first.pattern_positions. Note that it returns the FIRST iteration‘s value.

[Source]

# File lib/bio/appl/blast/format0.rb, line 178
        def pattern_positions
          @iterations.first.pattern_positions
        end

program()

Returns program name.

[Source]

# File lib/bio/appl/blast/format0.rb, line 156
        def program;        format0_parse_header; @program;        end

query_def()

Returns definition of the query.

[Source]

# File lib/bio/appl/blast/format0.rb, line 168
        def query_def; format0_parse_query; @query_def; end

query_len()

Returns length of the query.

[Source]

# File lib/bio/appl/blast/format0.rb, line 165
        def query_len; format0_parse_query; @query_len; end

reference()

Returns the bibliography reference of the BLAST software. Note that this method shows only the first reference. When you want to get additional references, you can use references method.

[Source]

# File lib/bio/appl/blast/format0.rb, line 229
        def reference
          references[0]
        end

references()

Returns the bibliography references of the BLAST software. Returns an array of strings.

[Source]

# File lib/bio/appl/blast/format0.rb, line 235
        def references
          unless defined?(@references)
            @references = @f0references.collect do |x|
              x.to_s.gsub(/\s+/, ' ').strip
            end
          end #unless
          @references
        end

to_s()

Returns whole entry as a string.

[Source]

# File lib/bio/appl/blast/format0.rb, line 74
        def to_s; @entry; end

version()

Returns version of the program.

[Source]

# File lib/bio/appl/blast/format0.rb, line 158
        def version;        format0_parse_header; @version;        end

version_date()

Returns released date of the program.

[Source]

# File lib/bio/appl/blast/format0.rb, line 162
        def version_date;   format0_parse_header; @version_date;   end

version_number()

Returns version number string of the program.

[Source]

# File lib/bio/appl/blast/format0.rb, line 160
        def version_number; format0_parse_header; @version_number; end

Methods

Classes and Modules

Constants

Attributes

Public Class methods

Public Instance methods