Class Bio::HMMER::Report
In: lib/bio/appl/hmmer/report.rb
Parent: Object

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

Methods

each   each_hit   new  

Classes and Modules

Class Bio::HMMER::Report::Hit
Class Bio::HMMER::Report::Hsp

Constants

DELIMITER = RS = "\n//\n"   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)

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"))

[Source]

     # File lib/bio/appl/hmmer/report.rb, line 156
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| ...}

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

[Source]

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

Alias for each

[Validate]