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.
Delimiter of each entry. Bio::FlatFile uses it.
(Integer) excess read size included in DELIMITER.
(PSI-BLAST) Returns iterations. It returns an array of Bio::Blast::Default::Report::Iteration class. Note that normal blastall result usually contains one iteration.
Creates a new Report object from BLAST result text.
# File lib/bio/appl/blast/format0.rb, line 48 def initialize(str) str = str.sub(/\A\s+/, '') str.sub!(/\n(T?BLAST.*)/, "\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
Opens file by using Bio::FlatFile.open.
# File lib/bio/appl/blast/format0.rb, line 43 def self.open(filename, *mode) Bio::FlatFile.open(self, filename, *mode) end
(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, line 203 def converged? @iterations.last.converged? end
Returns the name (filename or title) of the database.
# File lib/bio/appl/blast/format0.rb, line 227 def db unless defined?(@db) if /Database *\: *(.*)/ =~ @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
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, line 178 def each_hit @iterations.last.each do |x| yield x end end
(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, line 168 def each_iteration @iterations.each do |x| yield x end end
Same as iterations.last.entropy.
# File lib/bio/appl/blast/format0.rb, line 128 def entropy; @iterations.last.entropy; end
Same as iterations.last.gapped_entropy.
# File lib/bio/appl/blast/format0.rb, line 135 def gapped_entropy; @iterations.last.gapped_entropy; end
Same as iterations.last.gapped_kappa.
# File lib/bio/appl/blast/format0.rb, line 131 def gapped_kappa; @iterations.last.gapped_kappa; end
Same as iterations.last.gapped_lambda.
# File lib/bio/appl/blast/format0.rb, line 133 def gapped_lambda; @iterations.last.gapped_lambda; end
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, line 189 def hits @iterations.last.hits end
Same as iterations.last.kappa.
# File lib/bio/appl/blast/format0.rb, line 124 def kappa; @iterations.last.kappa; end
Same as iterations.last.lambda.
# File lib/bio/appl/blast/format0.rb, line 126 def lambda; @iterations.last.lambda; end
(PSI-BLAST) Same as iterations.last.message.
# File lib/bio/appl/blast/format0.rb, line 195 def message @iterations.last.message end
(PHI-BLAST) Same as iterations.first.pattern. Note that it returns the FIRST iteration’s value.
# File lib/bio/appl/blast/format0.rb, line 155 def pattern; @iterations.first.pattern; end
(PHI-BLAST) Same as iterations.first.pattern_positions. Note that it returns the FIRST iteration’s value.
# File lib/bio/appl/blast/format0.rb, line 160 def pattern_positions @iterations.first.pattern_positions end
Returns program name.
# File lib/bio/appl/blast/format0.rb, line 138 def program; format0_parse_header; @program; end
Returns definition of the query.
# File lib/bio/appl/blast/format0.rb, line 150 def query_def; format0_parse_query; @query_def; end
Returns length of the query.
# File lib/bio/appl/blast/format0.rb, line 147 def query_len; format0_parse_query; @query_len; end
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, line 211 def reference references[0] end
Returns the bibliography references of the BLAST software. Returns an array of strings.
# File lib/bio/appl/blast/format0.rb, line 217 def references unless defined?(@references) @references = @f0references.collect do |x| x.to_s.gsub(/\s+/, ' ').strip end end #unless @references end
Returns whole entry as a string.
# File lib/bio/appl/blast/format0.rb, line 69 def to_s; @entry; end
Returns version of the program.
# File lib/bio/appl/blast/format0.rb, line 140 def version; format0_parse_header; @version; end
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