A parser class for a search report by hmmsearch or hmmpfam program in the HMMER package.
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
Delimiter of each entry for Bio::FlatFile support.
statistics by hmmsearch. Keys are ‘Total memory’, ‘Satisfying E cutoff’ and ‘Total hits’.
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.
A Hash contains program information used. Valid keys are ‘name’, ‘version’, ‘copyright’ and ‘license’.
A hash contains the query information. Valid keys are ‘query sequence’, ‘Accession’ and ‘Description’.
Parses a HMMER search report (by hmmpfam or hmmsearch program) and reutrns a Bio::HMMER::Report object.
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, line 156 def initialize(data) # The input data is divided into six data fields, i.e. header, # query infomation, hits, HSPs, alignments and search statistics. # However, header and statistics data don't necessarily exist. subdata, is_hmmsearch = get_subdata(data) # if header exists, parse it if subdata["header"] @program, @parameter = parse_header_data(subdata["header"]) else @program, @parameter = [{}, {}] end @query_info = parse_query_info(subdata["query"]) @hits = parse_hit_data(subdata["hit"]) @hsps = parse_hsp_data(subdata["hsp"], is_hmmsearch) if @hsps != [] # split alignment subdata into an array of alignments aln_ary = subdata["alignment"].split(/^\S+.*?\n/).slice(1..-1) # append alignment information to corresponding Hsp aln_ary.each_with_index do |aln, i| @hsps[i].set_alignment(aln) end end # assign each Hsp object to its parent Hit hits_hash = {} @hits.each do |hit| hits_hash[hit.accession] = hit end @hsps.each do |hsp| if hits_hash.has_key?(hsp.accession) hits_hash[hsp.accession].append_hsp(hsp) end end # parse statistics (for hmmsearch) if is_hmmsearch @histogram, @statistical_detail, @total_seq_searched, @whole_seq_top_hits, @domain_top_hits = parse_stat_data(subdata["statistics"]) end end
Iterates each hit (Bio::HMMER::Report::Hit).
# File lib/bio/appl/hmmer/report.rb, line 206 def each @hits.each do |hit| yield hit end end
Generated with the Darkfish Rdoc Generator 2.