Class: BlastStreamxmlResult

Inherits:
BlastResult show all
Defined in:
lib/scbi_blast/blast_streamxml_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) ⇒ BlastStreamxmlResult

Parser initialization



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# File 'lib/scbi_blast/blast_streamxml_result.rb', line 15

def initialize(input)
  super(input)

  lines=[]
  
  # some variables for tracking the state of the parse
  @current_query = nil
  @current_hit = nil
  @current_element = nil
  @current_hit_subject_id=''
  @current_hit_acc=''
  @current_hit_full_subject_length=0
  @current_hit_hit_def=''
  
  # @state = nil # (values :in_query,:in_hit)
  
  return if input.empty?
  
  if input.is_a?(Array)
    lines=input.join("\n")
    do_parse(lines)
    
  elsif !input.strip.empty?
    
    if File.exists?(input)
      lines= File.open(input,'r')
      # @lines = fich.readlines
      # fich.close
      do_parse(lines)
      lines.close
    else
      raise "File #{input} doesn't exists"
    end
  end
  
end

Instance Method Details

#do_parse(lines) ⇒ Object 



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# File 'lib/scbi_blast/blast_streamxml_result.rb', line 178

def do_parse(lines)
  Document.parse_stream(lines, self)
end

#tag_end(name) ⇒ Object 



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# File 'lib/scbi_blast/blast_streamxml_result.rb', line 79

def tag_end(name)
  
  case name
    when 'Iteration'
      @querys.push @current_query
      @current_query=nil
    when 'Hit'
      @current_hit_subject_id=''
      @current_hit_acc=''
      @current_hit_full_subject_length=0
      @current_hit_hit_def=''
      @current_hit=nil
      
    when 'Hsp'
      @current_hit.set_limits(@current_hit.q_beg,@current_hit.q_end,@current_hit.s_beg,@current_hit.s_end)
      
      @current_query.hits.push @current_hit
      
  end
  
  @current_element=nil
  # puts "-#{name}"

end

#tag_start(name, attributes) ⇒ Object 



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# File 'lib/scbi_blast/blast_streamxml_result.rb', line 53

def tag_start(name, attributes)
  # puts "+#{name}: #{attributes}"
  case name
    when 'Iteration'
      @current_query= BlastQuery.new(-1)
      
    when 'Hit'
      @current_hit_subject_id=''
      @current_hit_acc=''
      @current_hit_full_subject_length=0
      @current_hit_hit_def=''
      
    when 'Hsp'
      @current_hit = BlastHit.new(0,0,0,0)
      
      # populate results from hit
      @current_hit.subject_id=@current_hit_subject_id
      @current_hit.full_subject_length=@current_hit_full_subject_length
      @current_hit.definition=@current_hit_hit_def
      @current_hit.acc=@current_hit_acc
    else
      @current_element = name
  end
  
end

#text(text) ⇒ Object 



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# File 'lib/scbi_blast/blast_streamxml_result.rb', line 104

def text(text)
  
  case @current_element
    
    # values for querys 
    when 'Iteration_query-ID'
      @current_query.query_id=text
    when 'Iteration_query-len'
      @current_query.full_query_length=text.to_i
    when 'Iteration_query-def'
      @current_query.query_def=text
      
    # values for hits
    when 'Hit_id'
      @current_hit_subject_id=text
    when 'Hit_accession'
      @current_hit_acc=text
    when 'Hit_len'
      @current_hit_full_subject_length=text.to_i
    when 'Hit_def'
      @current_hit_hit_def=text
      if @current_hit_hit_def=='No definition line'
        @current_hit_hit_def =@current_hit_subject_id
      end

    # values for HSPs
    

      when 'Hsp_query-from'
        # puts "QBEG1:#{text.to_i}"
        @current_hit.q_beg=text.to_i
        # puts "QBEG2:#{@current_hit.q_beg},#{text.to_i}"
      when 'Hsp_query-to'
        @current_hit.q_end=text.to_i
      when 'Hsp_hit-from'
        @current_hit.s_beg=text.to_i
      when 'Hsp_hit-to'
        @current_hit.s_end=text.to_i
      when 'Hsp_align-len'
        @current_hit.align_len=text.to_i
        @current_hit.ident=(@current_hit.ident/@current_hit.align_len)*100
      when 'Hsp_identity'
        
        @current_hit.ident=(text.to_f)
        # @current_hit.ident=(text.to_f/@current_hit.align_len)*100
        # percent calculation now goes to align-len
      when 'Hsp_gaps'
        @current_hit.gaps=text.to_i
      when 'Hsp_midline'
        @current_hit.mismatches= text.count(' ').to_i - @current_hit.gaps
      when 'Hsp_evalue'
        @current_hit.e_val=text.to_f
        @current_hit.e_val = (@current_hit.e_val*1000).round/1000.0
      when 'Hsp_bit-score'
        @current_hit.bit_score=text.to_f
        @current_hit.bit_score = (@current_hit.bit_score*100).round/100.0
      when 'Hsp_score'
        @current_hit.score =text.to_f
      when 'Hsp_query-frame'
        @current_hit.q_frame = text.to_i
      when 'Hsp_hit-frame'
        @current_hit.s_frame =text.to_i

      when 'Hsp_qseq'
        @current_hit.q_seq = text
      when 'Hsp_hseq'
        @current_hit.s_seq = text
    
  end

  # reset the current element so we don't pick up empty text
  @current_element = nil
end