Class: BlastXmlResult

Inherits:
Object
  • Object
show all
Defined in:
lib/scbi_blast/blast_xml_result.rb

Overview

Another XML parser using nokogiri library

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(input) ⇒ BlastXmlResult

Returns a new instance of BlastXmlResult.



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# File 'lib/scbi_blast/blast_xml_result.rb', line 31

def initialize(input)

  @querys = []
  lines=[]

  if input.is_a?(Array)
    lines=input
  else
    if File.exists?(input)
      fich = File.open(input,'r')
      lines = fich.readlines
      fich.close
    end

  end

  # puts "lines length #{lines.length}"
  if !lines.empty?
    data = Nokogiri::XML(lines.join)
    data.root.xpath('//Iteration').each do |iteration|

      # puts JSON::pretty_generate(iteration)
      query_id = iteration.xpath('Iteration_query-ID').text

      full_query_length = iteration.xpath('Iteration_query-len').text
      query_def = iteration.xpath('Iteration_query-def').text

      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.xpath('Iteration_hits/Hit')
      if !hits.nil?
        hits.each do |h|
          #puts JSON::pretty_generate(h)



          subject_id=h.xpath('Hit_id').text
          acc =h.xpath('Hit_accession').text
          full_subject_length = h.xpath('Hit_len').text.to_i
          hit_def=h.xpath('Hit_def').text
          if hit_def=='No definition line'
            hit_def =subject_id
          end

          hsps = h.xpath('Hit_hsps/Hsp')

          hsps.each do |hsp|

            q_beg=hsp.xpath('Hsp_query-from').text.to_i
            q_end=hsp.xpath('Hsp_query-to').text.to_i
            s_beg=hsp.xpath('Hsp_hit-from').text.to_i
            s_end=hsp.xpath('Hsp_hit-to').text.to_i

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

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

            hit.score = hsp.xpath('Hsp_score').text.to_f
            hit.q_frame = hsp.xpath('Hsp_query-frame').text.to_i
            hit.s_frame =hsp.xpath('Hsp_hit-frame').text.to_i

            hit.q_seq = hsp.xpath('Hsp_qseq').text
            hit.s_seq = hsp.xpath('Hsp_hseq').text


            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

Instance Attribute Details

#querys ⇒ Object

Returns the value of attribute querys.



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# File 'lib/scbi_blast/blast_xml_result.rb', line 162

def querys
  @querys
end

Instance Method Details

#empty? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/scbi_blast/blast_xml_result.rb', line 153

def empty?

  return @querys.empty?
end

#find_query(querys, name_q) ⇒ Object 



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# File 'lib/scbi_blast/blast_xml_result.rb', line 142

def find_query(querys,name_q)
  #  newq = querys.find{|q| ( q.find{|h| (h.subject_id)})}
  new_q=nil

  if !querys.empty?
    new_q=querys.find{|q| (q.query_id==name_q)}
  end

  return new_q
end

#inspect ⇒ Object 



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# File 'lib/scbi_blast/blast_xml_result.rb', line 133

def inspect

  res = "Blast results:\n"
  res+= '-'*20
  res+= "\nQuerys: #{@querys.count}\n"
  @querys.each{|q| res+=q.inspect+"\n"}
  return res
end

#size ⇒ Object 



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# File 'lib/scbi_blast/blast_xml_result.rb', line 158

def size
  @querys.size
end