Class: Bio::Blast::Report

Inherits:
Object show all
Defined in:
lib/bio/appl/blast/report.rb,
lib/bio/appl/blast/rexml.rb,
lib/bio/appl/blast/format8.rb,
lib/bio/appl/blast/xmlparser.rb

Overview

Bio::Blast::Report

Parsed results of the blast execution for Tab-delimited and XML output format. Tab-delimited reports are consists of

Query id,
Subject id,
percent of identity,
alignment length,
number of mismatches (not including gaps),
number of gap openings,
start of alignment in query,
end of alignment in query,
start of alignment in subject,
end of alignment in subject,
expected value,
bit score.

according to the MEGABLAST document (README.mbl). As for XML output, see the following DTDs.

* http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd
* http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.mod
* http://www.ncbi.nlm.nih.gov/dtd/NCBI_Entity.mod

Defined Under Namespace

Classes: Hit, Hsp, Iteration

Constant Summary collapse

DELIMITER =

for Bio::FlatFile support (only for XML data)

RS = "</BlastOutput>\n"

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(data, parser = nil) ⇒ Report

Passing a BLAST output from ‘blastall -m 7’ or ‘-m 8’ as a String. Formats are auto detected.



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# File 'lib/bio/appl/blast/report.rb', line 78

def initialize(data, parser = nil)
  @iterations = []
  @parameters = {}
  case parser
  when :xmlparser		# format 7
    xmlparser_parse(data)
  when :rexml		# format 7
    rexml_parse(data)
  when :tab		# format 8
    tab_parse(data)
  else
    auto_parse(data)
  end
end

Instance Attribute Details

#db ⇒ Object (readonly)

Shortcut for BlastOutput values.



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# File 'lib/bio/appl/blast/report.rb', line 102

def db
  @db
end

#iterations ⇒ Object (readonly)

Returns an Array of Bio::Blast::Report::Iteration objects.



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# File 'lib/bio/appl/blast/report.rb', line 94

def iterations
  @iterations
end

#parameters ⇒ Object (readonly)

Returns a Hash containing execution parameters. Valid keys are: ‘matrix’, ‘expect’, ‘include’, ‘sc-match’, ‘sc-mismatch’, ‘gap-open’, ‘gap-extend’, ‘filter’



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# File 'lib/bio/appl/blast/report.rb', line 99

def parameters
  @parameters
end

#program ⇒ Object (readonly)

Shortcut for BlastOutput values.



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# File 'lib/bio/appl/blast/report.rb', line 102

def program
  @program
end

#query_def ⇒ Object (readonly)

Shortcut for BlastOutput values.



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# File 'lib/bio/appl/blast/report.rb', line 102

def query_def
  @query_def
end

#query_id ⇒ Object (readonly)

Shortcut for BlastOutput values.



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# File 'lib/bio/appl/blast/report.rb', line 102

def query_id
  @query_id
end

#query_len ⇒ Object (readonly)

Shortcut for BlastOutput values.



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# File 'lib/bio/appl/blast/report.rb', line 102

def query_len
  @query_len
end

#reference ⇒ Object (readonly)

Shortcut for BlastOutput values.



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# File 'lib/bio/appl/blast/report.rb', line 102

def reference
  @reference
end

#version ⇒ Object (readonly)

Shortcut for BlastOutput values.



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# File 'lib/bio/appl/blast/report.rb', line 102

def version
  @version
end

Class Method Details

.rexml(data) ⇒ Object

Specify to use REXML to parse XML (-m 7) output.



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# File 'lib/bio/appl/blast/report.rb', line 54

def self.rexml(data)
  self.new(data, :rexml)
end

.tab(data) ⇒ Object

Specify to use tab delimited output parser.



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# File 'lib/bio/appl/blast/report.rb', line 59

def self.tab(data)
  self.new(data, :tab)
end

.xmlparser(data) ⇒ Object

Specify to use XMLParser to parse XML (-m 7) output.



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# File 'lib/bio/appl/blast/report.rb', line 49

def self.xmlparser(data)
  self.new(data, :xmlparser)
end

Instance Method Details

#db_len ⇒ Object

Length of BLAST db



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# File 'lib/bio/appl/blast/report.rb', line 158

def db_len;    statistics['db-len'];    end

#db_num ⇒ Object

Number of sequences in BLAST db



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# File 'lib/bio/appl/blast/report.rb', line 156

def db_num;    statistics['db-num'];    end

#each_hit ⇒ Object Also known as: each

Iterates on each Bio::Blast::Report::Hit object of the the last Iteration. Shortcut for the last iteration’s hits (for blastall)



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# File 'lib/bio/appl/blast/report.rb', line 134

def each_hit
  @iterations.last.each do |x|
    yield x
  end
end

#each_iteration ⇒ Object

Iterates on each Bio::Blast::Report::Iteration object. (for blastpgp)



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# File 'lib/bio/appl/blast/report.rb', line 126

def each_iteration
  @iterations.each do |x|
    yield x
  end
end

#eff_space ⇒ Object

Effective search space



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# File 'lib/bio/appl/blast/report.rb', line 162

def eff_space; statistics['eff-space']; end

#entrez_query ⇒ Object

Limit of request to Entrez : shortcuts for @parameters



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# File 'lib/bio/appl/blast/report.rb', line 123

def entrez_query; @parameters['entrez-query'];     end

#entropy ⇒ Object

Karlin-Altschul parameter H



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# File 'lib/bio/appl/blast/report.rb', line 168

def entropy;   statistics['entropy'];   end

#expect ⇒ Object

Expectation threshold (-e) : shortcuts for @parameters



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# File 'lib/bio/appl/blast/report.rb', line 107

def expect;       @parameters['expect'].to_i;      end

#filter ⇒ Object

Filtering options (-F) : shortcuts for @parameters



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# File 'lib/bio/appl/blast/report.rb', line 119

def filter;       @parameters['filter'];           end

#gap_extend ⇒ Object

Gap extension cost (-E) : shortcuts for @parameters



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# File 'lib/bio/appl/blast/report.rb', line 117

def gap_extend;   @parameters['gap-extend'].to_i;  end

#gap_open ⇒ Object

Gap opening cost (-G) : shortcuts for @parameters



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# File 'lib/bio/appl/blast/report.rb', line 115

def gap_open;     @parameters['gap-open'].to_i;    end

#hits ⇒ Object

Returns a Array of Bio::Blast::Report::Hits of the last iteration. Shortcut for the last iteration’s hits



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# File 'lib/bio/appl/blast/report.rb', line 143

def hits
  @iterations.last.hits
end

#hsp_len ⇒ Object

Effective HSP length



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# File 'lib/bio/appl/blast/report.rb', line 160

def hsp_len;   statistics['hsp-len'];   end

#inclusion ⇒ Object

Inclusion threshold (-h) : shortcuts for @parameters



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# File 'lib/bio/appl/blast/report.rb', line 109

def inclusion;    @parameters['include'].to_i;     end

#kappa ⇒ Object

Karlin-Altschul parameter K



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# File 'lib/bio/appl/blast/report.rb', line 164

def kappa;     statistics['kappa'];     end

#lambda ⇒ Object

Karlin-Altschul parameter Lamba



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# File 'lib/bio/appl/blast/report.rb', line 166

def lambda;    statistics['lambda'];    end

#matrix ⇒ Object

Matrix used (-M) : shortcuts for @parameters



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# File 'lib/bio/appl/blast/report.rb', line 105

def matrix;       @parameters['matrix'];           end

#message ⇒ Object

Returns a String (or nil) containing execution message of the last iteration (typically “CONVERGED”). Shortcut for the last iteration’s message (for checking ‘CONVERGED’)



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# File 'lib/bio/appl/blast/report.rb', line 173

def message
  @iterations.last.message
end

#pattern ⇒ Object

PHI-BLAST pattern : shortcuts for @parameters



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# File 'lib/bio/appl/blast/report.rb', line 121

def pattern;      @parameters['pattern'];          end

#sc_match ⇒ Object

Match score for NT (-r) : shortcuts for @parameters



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# File 'lib/bio/appl/blast/report.rb', line 111

def sc_match;     @parameters['sc-match'].to_i;    end

#sc_mismatch ⇒ Object

Mismatch score for NT (-q) : shortcuts for @parameters



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# File 'lib/bio/appl/blast/report.rb', line 113

def sc_mismatch;  @parameters['sc-mismatch'].to_i; end

#statistics ⇒ Object

Returns a Hash containing execution statistics of the last iteration. Valid keys are: ‘db-num’, ‘db-len’, ‘hsp-len’, ‘eff-space’, ‘kappa’, ‘lambda’, ‘entropy’ Shortcut for the last iteration’s statistics.



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# File 'lib/bio/appl/blast/report.rb', line 151

def statistics
  @iterations.last.statistics
end