class Bio::Blast::Default::Report

Bio::Blast::Default::Report parses NCBI BLAST default output and stores information in the data. It may store some Bio::Blast::Default::Report::Iteration objects.

Constants

DELIMITER: Delimiter of each entry. Bio::FlatFile uses it.
DELIMITER_OVERRUN: (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) click to toggle source

Creates a new Report object from BLAST result text.

   # File lib/bio/appl/blast/format0.rb
48 def initialize(str)
49   str = str.sub(/\A\s+/, '')
50   str.sub!(/\n(T?BLAST.*)/m, "\n") # remove trailing entries for sure
51   @entry_overrun = $1
52   @entry = str
53   data = str.split(/(?:^[ \t]*\n)+/)
54 
55   format0_split_headers(data)
56   @iterations = format0_split_search(data)
57   format0_split_stat_params(data)
58 end

open(filename, *mode) click to toggle source

Opens file by using Bio::FlatFile.open.

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

Public Instance Methods

converged?() click to toggle source

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

    # File lib/bio/appl/blast/format0.rb
203 def converged?
204   @iterations.last.converged?
205 end

db() click to toggle source

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

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

each()

Alias for: each_hit

each_hit() { |x| ... } click to toggle source

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.

    # File lib/bio/appl/blast/format0.rb
178 def each_hit
179   @iterations.last.each do |x|
180     yield x
181   end
182 end

Also aliased as: each

each_iteration() { |x| ... } click to toggle source

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

    # File lib/bio/appl/blast/format0.rb
168 def each_iteration
169   @iterations.each do |x|
170     yield x
171   end
172 end

entropy() click to toggle source

Same as iterations.last.entropy.

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

gapped_entropy() click to toggle source

Same as iterations.last.gapped_entropy.

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

gapped_kappa() click to toggle source

Same as iterations.last.gapped_kappa.

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

gapped_lambda() click to toggle source

Same as iterations.last.gapped_lambda.

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

hits() click to toggle source

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.

    # File lib/bio/appl/blast/format0.rb
189 def hits
190   @iterations.last.hits
191 end

kappa() click to toggle source

Same as iterations.last.kappa.

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

lambda() click to toggle source

Same as iterations.last.lambda.

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

message() click to toggle source

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

    # File lib/bio/appl/blast/format0.rb
195 def message
196   @iterations.last.message
197 end

pattern() click to toggle source

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

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

pattern_positions() click to toggle source

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

    # File lib/bio/appl/blast/format0.rb
160 def pattern_positions
161   @iterations.first.pattern_positions
162 end

program() click to toggle source

Returns program name.

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

query_def() click to toggle source

Returns definition of the query.

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

query_len() click to toggle source

Returns length of the query.

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

reference() click to toggle source

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.

    # File lib/bio/appl/blast/format0.rb
211 def reference
212   references[0]
213 end

references() click to toggle source

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

    # File lib/bio/appl/blast/format0.rb
217 def references
218   unless defined?(@references)
219     @references = @f0references.collect do |x|
220       x.to_s.gsub(/\s+/, ' ').strip
221     end
222   end #unless
223   @references
224 end

to_s() click to toggle source

Returns whole entry as a string.

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

version() click to toggle source

Returns version of the program.

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

version_date() click to toggle source

Returns released date of the program.

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

version_number() click to toggle source

Returns version number string of the program.

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