Class: Hit

Inherits:
Object
  • Object
show all
Defined in:
lib/gene_assembler/hit.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(hit_name, s_length, q_frame, type) ⇒ Hit

Returns a new instance of Hit.



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# File 'lib/gene_assembler/hit.rb', line 4

def initialize (hit_name, s_length, q_frame, type)
  @name=hit_name #Nombre tomado del subject_id

  #@s_seq=s_seq #Secuencia del subject

  #@q_seq=q_seq #Secuencia del query

  @s_length=s_length # Longitud total del subject

  @hsps=[]
  if q_frame>0
    @reversed=FALSE
  else
    @reversed=TRUE
  end
  @type=type
  @source=nil
  @description=nil
  @e_value=nil
  @q_p_ident=nil
  @q_p_conserved=nil
  
end

Instance Attribute Details

#description ⇒ Object

Returns the value of attribute description.



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# File 'lib/gene_assembler/hit.rb', line 3

def description
  @description
end

#e_value ⇒ Object

Returns the value of attribute e_value.



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# File 'lib/gene_assembler/hit.rb', line 3

def e_value
  @e_value
end

#hsps ⇒ Object

Returns the value of attribute hsps.



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# File 'lib/gene_assembler/hit.rb', line 3

def hsps
  @hsps
end

#name ⇒ Object

Returns the value of attribute name.



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# File 'lib/gene_assembler/hit.rb', line 3

def name
  @name
end

#q_p_conserved ⇒ Object

Returns the value of attribute q_p_conserved.



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# File 'lib/gene_assembler/hit.rb', line 3

def q_p_conserved
  @q_p_conserved
end

#q_p_ident ⇒ Object

Returns the value of attribute q_p_ident.



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# File 'lib/gene_assembler/hit.rb', line 3

def q_p_ident
  @q_p_ident
end

#reversed ⇒ Object

Returns the value of attribute reversed.



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# File 'lib/gene_assembler/hit.rb', line 3

def reversed
  @reversed
end

#s_length ⇒ Object

Returns the value of attribute s_length.



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# File 'lib/gene_assembler/hit.rb', line 3

def s_length
  @s_length
end

#source ⇒ Object

Returns the value of attribute source.



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# File 'lib/gene_assembler/hit.rb', line 3

def source
  @source
end

#type ⇒ Object

Returns the value of attribute type.



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# File 'lib/gene_assembler/hit.rb', line 3

def type
  @type
end

Instance Method Details

#add_hsp(q_beg, q_end, s_beg, s_end, align_len, score, ident, gaps) ⇒ Object 



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# File 'lib/gene_assembler/hit.rb', line 24

def add_hsp(q_beg, q_end, s_beg, s_end, align_len, score, ident, gaps)
  hsp= Hsp.new(q_beg, q_end, s_beg, s_end, align_len, score, ident, gaps)
  @hsps << hsp
  return hsp
end

#correct_hsps(blast_coor_type) ⇒ Object

‘s’ => subject, ‘q’ => query



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# File 'lib/gene_assembler/hit.rb', line 148

def correct_hsps(blast_coor_type)# 's' => subject, 'q' => query 

#   puts self.inspect

   if hsp_count>1
    delete_hsps=[]
    each_hsp_with_index{|hsp,i|
      each_hsp_with_index{|hsp_second,j|
        if i==j
          next
        end
#         puts hsp.compare(hsp_second)

         compare=nil
         if blast_coor_type == 's'
           compare = hsp.compare(hsp_second)
         else
           compare = hsp.compare_q(hsp_second)
         end
        if compare >= 0.9
          if hsp.score == hsp_second.score # En caso de hsps con scores iguales, nos quedamos con el mas pequeño

            if hsp.align_len == hsp_second.align_len # Si dos hsps son exactamente iguales eliminamos el segundo

              delete_hsps << j
            elsif hsp.align_len < hsp_second.align_len
              delete_hsps << j
            else
              delete_hsps << i
            end           
          elsif hsp.score > hsp_second.score
            delete_hsps << j
          else
            delete_hsps << i
          end
        end
      }
    }
    delete_hsps.uniq!
    delete_hsps.reverse_each do |hsp|
      drop_hsp(hsp)
    end
  end
end

#drop_hsp(position) ⇒ Object 



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# File 'lib/gene_assembler/hit.rb', line 188

def drop_hsp(position)
  hsps.delete_at(position)
end

#each_hsp ⇒ Object 



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# File 'lib/gene_assembler/hit.rb', line 30

def each_hsp
  @hsps.each do |hsp|
    yield hsp
  end
end

#each_hsp_with_index ⇒ Object 



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# File 'lib/gene_assembler/hit.rb', line 47

def each_hsp_with_index
  @hsps.each_with_index do |hsp,i|
    yield hsp,i
  end
end

#first_hsp ⇒ Object 



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# File 'lib/gene_assembler/hit.rb', line 65

def first_hsp
  h=nil
  each_hsp{|hit|
     h=hit
     break
  }
  return h
end

#hsp_at(n) ⇒ Object 



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# File 'lib/gene_assembler/hit.rb', line 36

def hsp_at(n)
  hsp_at=nil
  each_hsp_with_index{|hsp,i|
    if n==i
      hsp_at=hsp
      break
    end
  }
  return hsp_at
end

#hsp_count ⇒ Object 



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# File 'lib/gene_assembler/hit.rb', line 57

def hsp_count
  n=0
  each_hsp{|hsp|
    n+=1
  }
  return n
end

#hsp_minor_than?(hsp_length) ⇒ Boolean

En nt

Returns:

  • (Boolean) 


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# File 'lib/gene_assembler/hit.rb', line 137

def hsp_minor_than?(hsp_length)# En nt

  minor=FALSE
  each_hsp {|hsp|
    if hsp.length_q < hsp_length
      minor=TRUE
      break
    end 
  }
  return minor
end

#hsp_overlap ⇒ Object 



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# File 'lib/gene_assembler/hit.rb', line 111

def hsp_overlap
  overlap=[]
  last_hsp=nil
  each_hsp_with_index{|hsp,i|
    if i>0
      diference=hsp.overlap_with(last_hsp)
      if diference<0
        overlap << diference
      end
    end
    last_hsp=hsp
   }
   return overlap
end

#hsps_correlative? ⇒ Boolean

Ver si los hsps del hit son contiguos en la query

Returns:

  • (Boolean) 


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# File 'lib/gene_assembler/hit.rb', line 82

def hsps_correlative?  # Ver si los hsps del hit son contiguos en la query

  is_correlative=FALSE
  ends=0
  each_hsp_with_index{|hsp,i|
    if i==0
      ends=hsp.q_end
      next
    end
    if (ends-hsp.q_beg).abs>3
      is_correlative=TRUE
      break
    end
    ends=hsp.q_end
  }
  return is_correlative
end

#hsps_sort! ⇒ Object

Se ordenan los hsps en base a posicion en el subject



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# File 'lib/gene_assembler/hit.rb', line 53

def hsps_sort! # Se ordenan los hsps en base a posicion en el subject

  @hsps.sort!{|e1,e2| e1.s_beg<=>e2.s_beg}
end

#last_hsp ⇒ Object 



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# File 'lib/gene_assembler/hit.rb', line 74

def last_hsp
  h=nil
  each_hsp{|hit|
     h=hit
  }
  return h
end

#modified_coordenates(add) ⇒ Object 



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# File 'lib/gene_assembler/hit.rb', line 99

def modified_coordenates(add)
  each_hsp{|hsp|
    hsp.modified_coordenates(add)
  }
end

#overlap_with(last_hit) ⇒ Object 



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# File 'lib/gene_assembler/hit.rb', line 126

def overlap_with(last_hit)
  overlap=0
  if self.name==last_hit.name
    diference=self.first_hsp.overlap_with(last_hit.last_hsp)
    if diference<0
      overlap=diference
    end
  end
  return overlap
end

#rev_coord(contig_length) ⇒ Object 



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# File 'lib/gene_assembler/hit.rb', line 105

def rev_coord(contig_length)
  each_hsp{|hsp|
    hsp.rev_coord(contig_length)
  }
end