class Bio::Blast::Report

`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

Constants

DELIMITER: for Bio::FlatFile support (only for XML data)
FLATFILE_SPLITTER: Flatfile splitter for NCBI BLAST XML format. It is internally used when reading BLAST XML. Normally, users do not need to use it directly.

Attributes

db [R]

database name or title (String)

iterations [R]

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

parameters [R]

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

program [R]

program name (e.g. “blastp”) (String)

query_def [R]

query definition line (String)

query_id [R]

query ID (String)

query_len [R]

query length (Integer)

reference [R]

reference (String)

reports [R]

When the report contains results for multiple query sequences, returns an array of Bio::Blast::Report objects corresponding to the multiple queries. Otherwise, returns nil.

Note for “No hits found”: When no hits found for a query sequence, the result for the query is completely void and no information available in the result XML, including query ID and query definition. The only trace is that iteration number is skipped. This means that if the no-hit query is the last query, the query can not be detected, because the result XML is completely the same as the result XML without the query.

version [R]

BLAST version (e.g. “blastp 2.2.18 [Mar-02-2008]”) (String)

Public Class Methods

new (data, parser = nil)

Source

    # File lib/bio/appl/blast/report.rb
 87 def initialize(data, parser = nil)
 88   @iterations = []
 89   @parameters = {}
 90   case parser
 91   when :xmlparser             # format 7
 92     if defined? xmlparser_parse
 93       xmlparser_parse(data)
 94     else
 95       raise NameError, "xmlparser_parse does not defined"
 96     end
 97     @reports = blastxml_split_reports
 98   when :rexml         # format 7
 99     rexml_parse(data)
100     @reports = blastxml_split_reports
101   when :tab           # format 8
102     tab_parse(data)
103   when false
104     # do not parse, creates an empty object
105   else
106     auto_parse(data)
107   end
108 end

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

rexml (data)

Source

   # File lib/bio/appl/blast/report.rb
61 def self.rexml(data)
62   self.new(data, :rexml)
63 end

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

tab (data)

Source

   # File lib/bio/appl/blast/report.rb
66 def self.tab(data)
67   self.new(data, :tab)
68 end

Specify to use tab delimited output parser.

Public Instance Methods

db_len ()

Source

    # File lib/bio/appl/blast/report.rb
197 def db_len;    statistics['db-len'];    end

Length of BLAST db

db_num ()

Source

    # File lib/bio/appl/blast/report.rb
195 def db_num;    statistics['db-num'];    end

Number of sequences in BLAST db

each ()

Alias for: each_hit

each_hit () { |x| ... }

Source

    # File lib/bio/appl/blast/report.rb
173 def each_hit
174   @iterations.last.each do |x|
175     yield x
176   end
177 end

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

Also aliased as: each

each_iteration () { |x| ... }

Source

    # File lib/bio/appl/blast/report.rb
165 def each_iteration
166   @iterations.each do |x|
167     yield x
168   end
169 end

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

eff_space ()

Source

    # File lib/bio/appl/blast/report.rb
201 def eff_space; statistics['eff-space']; end

Effective search space

entrez_query ()

Source

    # File lib/bio/appl/blast/report.rb
162 def entrez_query; @parameters['entrez-query'];     end

Limit of request to Entrez : shortcuts for @parameters

entropy ()

Source

    # File lib/bio/appl/blast/report.rb
207 def entropy;   statistics['entropy'];   end

Karlin-Altschul parameter H

expect ()

Source

    # File lib/bio/appl/blast/report.rb
146 def expect;       @parameters['expect'];           end

Expectation threshold (-e) : shortcuts for @parameters

filter ()

Source

    # File lib/bio/appl/blast/report.rb
158 def filter;       @parameters['filter'];           end

Filtering options (-F) : shortcuts for @parameters

gap_extend ()

Source

    # File lib/bio/appl/blast/report.rb
156 def gap_extend;   @parameters['gap-extend'];       end

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

gap_open ()

Source

    # File lib/bio/appl/blast/report.rb
154 def gap_open;     @parameters['gap-open'];         end

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

hits ()

Source

    # File lib/bio/appl/blast/report.rb
182 def hits
183   @iterations.last.hits
184 end

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

hsp_len ()

Source

    # File lib/bio/appl/blast/report.rb
199 def hsp_len;   statistics['hsp-len'];   end

Effective HSP length

inclusion ()

Source

    # File lib/bio/appl/blast/report.rb
148 def inclusion;    @parameters['include'];          end

Inclusion threshold (-h) : shortcuts for @parameters

kappa ()

Source

    # File lib/bio/appl/blast/report.rb
203 def kappa;     statistics['kappa'];     end

Karlin-Altschul parameter K

lambda ()

Source

    # File lib/bio/appl/blast/report.rb
205 def lambda;    statistics['lambda'];    end

Karlin-Altschul parameter Lamba

matrix ()

Source

    # File lib/bio/appl/blast/report.rb
144 def matrix;       @parameters['matrix'];           end

Matrix used (-M) : shortcuts for @parameters

message ()

Source

    # File lib/bio/appl/blast/report.rb
212 def message
213   @iterations.last.message
214 end

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

pattern ()

Source

    # File lib/bio/appl/blast/report.rb
160 def pattern;      @parameters['pattern'];          end

PHI-BLAST pattern : shortcuts for @parameters

sc_match ()

Source

    # File lib/bio/appl/blast/report.rb
150 def sc_match;     @parameters['sc-match'];         end

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

sc_mismatch ()

Source

    # File lib/bio/appl/blast/report.rb
152 def sc_mismatch;  @parameters['sc-mismatch'];      end

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

statistics ()

Source

    # File lib/bio/appl/blast/report.rb
190 def statistics
191   @iterations.last.statistics
192 end

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.

class Bio::Blast::Report

Bio::Blast::Report¶ ↑

`Bio::Blast::Report`¶ ↑