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
for Bio::FlatFile support (only for XML data)
splitter for Bio::FlatFile support
Returns a Hash containing execution parameters. Valid keys are: 'matrix', 'expect', 'include', 'sc-match', 'sc-mismatch', 'gap-open', 'gap-extend', 'filter'
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.
Passing a BLAST output from 'blastall -m 7' or '-m 8' as a String. Formats are auto detected.
# File lib/bio/appl/blast/report.rb, line 85 def initialize(data, parser = nil) @iterations = [] @parameters = {} case parser when :xmlparser # format 7 xmlparser_parse(data) @reports = blastxml_split_reports when :rexml # format 7 rexml_parse(data) @reports = blastxml_split_reports when :tab # format 8 tab_parse(data) when false # do not parse, creates an empty object else auto_parse(data) end end
Specify to use REXML to parse XML (-m 7) output.
# File lib/bio/appl/blast/report.rb, line 59 def self.rexml(data) self.new(data, :rexml) end
Length of BLAST db
# File lib/bio/appl/blast/report.rb, line 191 def db_len; statistics['db-len']; end
Number of sequences in BLAST db
# File lib/bio/appl/blast/report.rb, line 189 def db_num; statistics['db-num']; end
Iterates on each Bio::Blast::Report::Hit object of the the last Iteration. Shortcut for the last iteration's hits (for blastall)
# File lib/bio/appl/blast/report.rb, line 167 def each_hit @iterations.last.each do |x| yield x end end
Iterates on each Bio::Blast::Report::Iteration object. (for blastpgp)
# File lib/bio/appl/blast/report.rb, line 159 def each_iteration @iterations.each do |x| yield x end end
Effective search space
# File lib/bio/appl/blast/report.rb, line 195 def eff_space; statistics['eff-space']; end
Limit of request to Entrez : shortcuts for @parameters
# File lib/bio/appl/blast/report.rb, line 156 def entrez_query; @parameters['entrez-query']; end
Karlin-Altschul parameter H
# File lib/bio/appl/blast/report.rb, line 201 def entropy; statistics['entropy']; end
Expectation threshold (-e) : shortcuts for @parameters
# File lib/bio/appl/blast/report.rb, line 140 def expect; @parameters['expect']; end
Filtering options (-F) : shortcuts for @parameters
# File lib/bio/appl/blast/report.rb, line 152 def filter; @parameters['filter']; end
Gap extension cost (-E) : shortcuts for @parameters
# File lib/bio/appl/blast/report.rb, line 150 def gap_extend; @parameters['gap-extend']; end
Gap opening cost (-G) : shortcuts for @parameters
# File lib/bio/appl/blast/report.rb, line 148 def gap_open; @parameters['gap-open']; end
Returns a Array of Bio::Blast::Report::Hits of the last iteration. Shortcut for the last iteration's hits
# File lib/bio/appl/blast/report.rb, line 176 def hits @iterations.last.hits end
Effective HSP length
# File lib/bio/appl/blast/report.rb, line 193 def hsp_len; statistics['hsp-len']; end
Inclusion threshold (-h) : shortcuts for @parameters
# File lib/bio/appl/blast/report.rb, line 142 def inclusion; @parameters['include']; end
Karlin-Altschul parameter K
# File lib/bio/appl/blast/report.rb, line 197 def kappa; statistics['kappa']; end
Karlin-Altschul parameter Lamba
# File lib/bio/appl/blast/report.rb, line 199 def lambda; statistics['lambda']; end
Matrix used (-M) : shortcuts for @parameters
# File lib/bio/appl/blast/report.rb, line 138 def matrix; @parameters['matrix']; 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')
# File lib/bio/appl/blast/report.rb, line 206 def message @iterations.last.message end
PHI-BLAST pattern : shortcuts for @parameters
# File lib/bio/appl/blast/report.rb, line 154 def pattern; @parameters['pattern']; end
Match score for NT (-r) : shortcuts for @parameters
# File lib/bio/appl/blast/report.rb, line 144 def sc_match; @parameters['sc-match']; end
Mismatch score for NT (-q) : shortcuts for @parameters
# File lib/bio/appl/blast/report.rb, line 146 def sc_mismatch; @parameters['sc-mismatch']; 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.
# File lib/bio/appl/blast/report.rb, line 184 def statistics @iterations.last.statistics end
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