class Bio::HMMER::Report

A parser class for a search report by hmmsearch or hmmpfam program in the HMMER package.

Examples ↑

Examples
 #for multiple reports in a single output file (example.hmmpfam)
 Bio::HMMER.reports(File.read("example.hmmpfam")) do |report|
   report.program['name']
   report.parameter['HMM file']
   report.query_info['Query sequence']
   report.hits.each do |hit|
     hit.accession
     hit.description
     hit.score
     hit.evalue
     hit.hsps.each do |hsp|
       hsp.accession
       hsp.domain
       hsp.evalue
       hsp.midline
   end
 end

References ↑

Constants

DELIMITER

Delimiter of each entry for Bio::FlatFile support.

Attributes

domain_top_hits[R]

statistics by hmmsearch. Keys are ‘Total memory’, ‘Satisfying E cutoff’ and ‘Total hits’.

histogram[R]

statistics by hmmsearch.

hits[R]
hsps[R]

Returns an Array of Bio::HMMER::Report::Hsp objects. Under special circumstances, some HSPs do not have parent Hit objects. If you want to access such HSPs, use this method.

parameter[R]

A hash contains parameters used. Valid keys are ‘HMM file’ and ‘Sequence file’.

program[R]

A Hash contains program information used. Valid keys are ‘name’, ‘version’, ‘copyright’ and ‘license’.

query_info[R]

A hash contains the query information. Valid keys are ‘query sequence’, ‘Accession’ and ‘Description’.

statistical_detail[R]

statistics by hmmsearch. Keys are ‘mu’, ‘lambda’, ‘chi-sq statistic’ and ‘P(chi-square)’.

total_seq_searched[R]

statistics by hmmsearch.

whole_seq_top_hits[R]

statistics by hmmsearch. Keys are ‘Total memory’, ‘Satisfying E cutoff’ and ‘Total hits’.

Public Class Methods

new(data) click to toggle source

Parses a HMMER search report (by hmmpfam or hmmsearch program) and reutrns a Bio::HMMER::Report object.

Examples ↑

hmmpfam_report = Bio::HMMER::Report.new(File.read("hmmpfam.out"))

hmmsearch_report = Bio::HMMER::Report.new(File.read("hmmsearch.out"))

    # File lib/bio/appl/hmmer/report.rb
156 def initialize(data)
157 
158   # The input data is divided into six data fields, i.e. header,
159   # query infomation, hits, HSPs, alignments and search statistics.
160   # However, header and statistics data don't necessarily exist.
161   subdata, is_hmmsearch = get_subdata(data)
162 
163   # if header exists, parse it
164   if subdata["header"]
165     @program, @parameter = parse_header_data(subdata["header"])
166   else
167     @program, @parameter = [{}, {}]
168   end
169 
170   @query_info = parse_query_info(subdata["query"])
171   @hits       = parse_hit_data(subdata["hit"])
172   @hsps       = parse_hsp_data(subdata["hsp"], is_hmmsearch)
173 
174   if @hsps != []
175     # split alignment subdata into an array of alignments
176     aln_ary = subdata["alignment"].split(/^\S+.*?\n/).slice(1..-1)
177 
178     # append alignment information to corresponding Hsp
179     aln_ary.each_with_index do |aln, i|
180       @hsps[i].set_alignment(aln)
181     end
182   end
183 
184   # assign each Hsp object to its parent Hit
185   hits_hash = {}
186   @hits.each do |hit|
187     hits_hash[hit.accession] = hit
188   end
189   @hsps.each do |hsp|
190     if hits_hash.has_key?(hsp.accession)
191       hits_hash[hsp.accession].append_hsp(hsp)
192     end
193   end
194 
195   # parse statistics (for hmmsearch)
196   if is_hmmsearch
197     @histogram, @statistical_detail, @total_seq_searched, \
198     @whole_seq_top_hits, @domain_top_hits = \
199     parse_stat_data(subdata["statistics"])
200   end
201 
202 end

Public Instance Methods

each() { |hit| ... } click to toggle source

Iterates each hit (Bio::HMMER::Report::Hit).

    # File lib/bio/appl/hmmer/report.rb
206 def each
207   @hits.each do |hit|
208     yield hit
209   end
210 end
Also aliased as: each_hit
each_hit()
Alias for: each