Class: BlastSimplexmlResult

Inherits:
BlastResult show all
Defined in:
lib/scbi_blast/blast_simplexml_result.rb

Overview

Extracts results from a blast results in XML format and uses it to create instances of “BlastQuery” and “BlastHit”

Instance Attribute Summary

Attributes inherited from BlastResult

#querys

Instance Method Summary collapse

Methods inherited from BlastResult

#compare?, #empty?, #find_query, #inspect, #size

Constructor Details

#initialize(input) ⇒ BlastSimplexmlResult

Parser initialization



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# File 'lib/scbi_blast/blast_simplexml_result.rb', line 33

def initialize(input)
  super(input)

  lines=[]
  if input.is_a?(Array)
    lines=input
  elsif !input.strip.empty?
    if File.exists?(input)
      fich = File.open(input,'r')
      lines = fich.readlines
      fich.close
    else
      raise "File #{input} doesn't exists"
    end
  end
  parse(lines)
end

Instance Method Details

#parse(lines) ⇒ Object 



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# File 'lib/scbi_blast/blast_simplexml_result.rb', line 51

def parse(lines)

  # puts "lines length #{lines.length}"
  if !lines.empty?
    data = XmlSimple.xml_in(lines.join)
    iterations = data['BlastOutput_iterations']
    #require 'json'
    #puts iterations.to_json

    iterations[0]['Iteration'].each do |iteration|

      # puts JSON::pretty_generate(iteration)

      query_id = iteration['Iteration_query-ID'][0]
      full_query_length = iteration['Iteration_query-len'][0].to_i
      query_def = iteration['Iteration_query-def'][0]

      if query_def =~ /^([^\s]+)/
        query_def=$1
      end
      

      #@query_def = iteration['Iteration_query-def'][0]

      query = BlastQuery.new(query_id)
      query.query_def = query_def
      query.full_query_length = full_query_length
      @querys.push query



      hits = iteration['Iteration_hits'][0]['Hit']
      if !hits.nil?
        hits.each do |h|
          #puts JSON::pretty_generate(h)



          subject_id=h['Hit_id'][0]
          acc =h['Hit_accession'][0]
          full_subject_length = h['Hit_len'][0].to_i
          hit_def=h['Hit_def'][0]
          if hit_def=='No definition line'
            hit_def =subject_id
          end

          hsps = h['Hit_hsps'][0]['Hsp']

          hsps.each do |hsp|

            q_beg=hsp['Hsp_query-from'][0].to_i
            q_end=hsp['Hsp_query-to'][0].to_i
            s_beg=hsp['Hsp_hit-from'][0].to_i
            s_end=hsp['Hsp_hit-to'][0].to_i

            # creates the hit
            hit = BlastHit.new(q_beg,q_end,s_beg,s_end)

            hit.align_len=hsp['Hsp_align-len'][0].to_i
            hit.ident=(hsp['Hsp_identity'][0].to_f/hit.align_len)*100
            hit.gaps=hsp['Hsp_gaps'][0].to_i
            hit.mismatches=hsp['Hsp_midline'][0].count(' ').to_i - hit.gaps
            hit.e_val=hsp['Hsp_evalue'][0].to_f
            hit.e_val = (hit.e_val*1000).round/1000.0
            hit.bit_score=hsp['Hsp_bit-score'][0].to_f
            hit.bit_score = (hit.bit_score*100).round/100.0

            hit.score = hsp['Hsp_score'][0].to_f
            hit.q_frame = hsp['Hsp_query-frame'][0].to_i
            hit.s_frame =hsp['Hsp_hit-frame'][0].to_i

            hit.q_seq = hsp['Hsp_qseq'][0]
            hit.s_seq = hsp['Hsp_hseq'][0]


            hit.subject_id= subject_id
            hit.full_subject_length=full_subject_length
            # hit.full_query_length = full_query_length
            hit.definition=hit_def
            hit.acc=acc

            query.add_hit(hit)

          end
        end
      end
    end
  end
  #inspect
end