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, line 48
def initialize(str)
  str = str.sub(%r\A\s+/, '')
  str.sub!(%r\n(T?BLAST.*)/, "\n") # remove trailing entries for sure
  @entry_overrun = $1
  @entry = str
  data = str.split(%r(?:^[ \t]*\n)+/)

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

open(filename, *mode) click to toggle source

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

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, line 203
def converged?
  @iterations.last.converged?
end

db() click to toggle source

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

# File lib/bio/appl/blast/format0.rb, line 227
def db
  unless defined?(@db)
    if %rDatabase *\: *(.*)/ =~ @f0database then
      a = $1.split(%r^/)
      a.pop if a.size > 1
      @db = a.collect { |x| x.sub(%r\s+\z/, '') }.join(' ')
    end
  end #unless
  @db
end

each() click to toggle source

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, line 178
def each_hit
  @iterations.last.each do |x|
    yield x
  end
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, line 168
def each_iteration
  @iterations.each do |x|
    yield x
  end
end

entropy() click to toggle source

Same as iterations.last.entropy.

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

kappa() click to toggle source

Same as iterations.last.kappa.

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

lambda() click to toggle source

Same as iterations.last.lambda.

# File lib/bio/appl/blast/format0.rb, line 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, line 195
def message
  @iterations.last.message
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, line 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, line 160
def pattern_positions
  @iterations.first.pattern_positions
end

program() click to toggle source

Returns program name.

# File lib/bio/appl/blast/format0.rb, line 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, line 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, line 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, line 211
def reference
  references[0]
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, line 217
def references
  unless defined?(@references)
    @references = @f0references.collect do |x|
      x.to_s.gsub(%r\s+/, ' ').strip
    end
  end #unless
  @references
end

to_s() click to toggle source

Returns whole entry as a string.

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

version() click to toggle source

Returns version of the program.

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