Class: Contig

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(name) ⇒ Contig

Returns a new instance of Contig.



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# File 'lib/gene_assembler/contig.rb', line 8

def initialize (name)
  @name=name
  @seq=''
  @type=nil
  @length=''
  @hits=[]
  @snps=[]
  @gos=[]
  @completed=''
  @localization=[]
  @q_frameshift=[]
  @s_frameshift=[]
  @stops=[]
  @mod_coord=FALSE #Indica si se han alterado las coordenadas del contig previamente

end

Instance Attribute Details

#completed ⇒ Object

Returns the value of attribute completed.



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# File 'lib/gene_assembler/contig.rb', line 7

def completed
  @completed
end

#hits ⇒ Object

Returns the value of attribute hits.



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# File 'lib/gene_assembler/contig.rb', line 7

def hits
  @hits
end

#length ⇒ Object

Returns the value of attribute length.



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# File 'lib/gene_assembler/contig.rb', line 7

def length
  @length
end

#mod_coord ⇒ Object

Returns the value of attribute mod_coord.



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# File 'lib/gene_assembler/contig.rb', line 7

def mod_coord
  @mod_coord
end

#name ⇒ Object

Returns the value of attribute name.



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# File 'lib/gene_assembler/contig.rb', line 7

def name
  @name
end

#q_frameshift ⇒ Object

Returns the value of attribute q_frameshift.



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# File 'lib/gene_assembler/contig.rb', line 7

def q_frameshift
  @q_frameshift
end

#s_frameshift ⇒ Object

Returns the value of attribute s_frameshift.



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# File 'lib/gene_assembler/contig.rb', line 7

def s_frameshift
  @s_frameshift
end

#seq ⇒ Object

Returns the value of attribute seq.



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# File 'lib/gene_assembler/contig.rb', line 7

def seq
  @seq
end

#stops ⇒ Object

Returns the value of attribute stops.



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# File 'lib/gene_assembler/contig.rb', line 7

def stops
  @stops
end

#type ⇒ Object

Returns the value of attribute type.



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# File 'lib/gene_assembler/contig.rb', line 7

def type
  @type
end

Instance Method Details

#add_go(go, name, obsolete) ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 85

def add_go(go,name,obsolete)
  go=GO.new(go,name,obsolete)
  @gos << go
  return go
end

#add_hit(hit_name, s_length, reversed, type) ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 103

def add_hit(hit_name, s_length, reversed, type)
  hit=Hit.new(hit_name, s_length, reversed, type)
  @hits << hit
  return hit
end

#add_localization(localization) ⇒ Object 



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

def add_localization(localization)
  @localization << localization
end

#add_snp(position) ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 97

def add_snp(position)
  snp=SNP.new(position)
  @snps << snp
  return snp
end

#compare(contig) ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 357

def compare(contig) #Alinea un contig con otro en base a las coordenadas del subject

  exon_match=-1
  exones=0
    match_found=FALSE
  #SELF HIT

  self.each_hit {|self_hit|
     if match_found #Romper bucle si ha habido coindidencia definitiva

       break
     end
      #SELF HSP

      self_hit.each_hsp {|self_hsp|
       if match_found
         break
       end
        #CONTIG HIT

        last=0
        contig_hsp_count=0
        contig.each_hit {|contig_hit|
          #CONTIG HSP

          contig_hit.each_hsp {|contig_hsp|#Valoracion del coverage de cada hit entre si, en el momento que el segundo de mayor se cancela

            coverage=self_hsp.compare(contig_hsp)
            if coverage>last #Guardar coincidencia a la espera de una mejor

              exon_match=contig_hsp_count
              last=coverage
            end
            if coverage>0.2 #Contaje de exones

              exones+=1
            end 
            if coverage==0 && exon_match>-1  #Romper bucle cuando se ha encontrado coincidencia y los demas exones no coinciden

              match_found=TRUE
              break
            end
            contig_hsp_count+=1
          }
          if match_found
            break
          end
         }
     }
  }
  return exon_match,exones
end

#coor_intrones ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 507

def coor_intrones
  #Determinar bordes de los intrones

  intrones=[]
  last_hsp=nil
  if first_hit.hsp_count>1
    first_hit.each_hsp_with_index{|hsp,i|
      if i>0
        intrones << [last_hsp.q_end,hsp.q_beg]
      end
      last_hsp=hsp
    }
  end
  #---------------------------------

  return intrones
end

#correct_hsps(blast_coor_type) ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 350

def correct_hsps(blast_coor_type)
  each_hit {|hit|
    hit.correct_hsps(blast_coor_type)
  }
end

#draw ⇒ Object

Realiza una representacion del contig a nivel del subject



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# File 'lib/gene_assembler/contig.rb', line 180

def draw #Realiza una representacion del contig a nivel del subject

  last_hsp_end=0
  overlap=0
  first_hit.each_hsp_with_index{|hsp,c|
    dif=hsp.s_beg-last_hsp_end
    if dif>=0 && dif<=2
      print '/' # Limite solapante uno a continuacion de otro (disposicion normal del exon)

    elsif dif>2
      print '-'*(hsp.s_beg-last_hsp_end)
      print '|'
    elsif dif<0
      print '&'
      overlap=dif
    end
    h=c+1 #Num de hsp

    print "#{h.to_s.center(hsp.s_end-hsp.s_beg+overlap-1)}"
    if dif>2
      #print '|'

    end
    last_hsp_end=hsp.s_end
  }
  print '|-'
  ending=first_hit.s_length-last_hsp_end
  if ending<0
    ending=0
  end
  print '-'*(ending)
  puts "\n"
end

#each_go ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 91

def each_go
  @gos.each do |go|
    yield go
  end
end

#each_hit ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 117

def each_hit
  @hits.each do |hit|
    yield hit
  end
end

#each_hit_with_index ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 123

def each_hit_with_index
  @hits.each_with_index do |hit,i|
    yield hit,i
  end
end

#each_localization ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 61

def each_localization
  @localization.each do |localization|
    yield localization
  end
end

#each_localization_with_index ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 67

def each_localization_with_index
  @localization.each_with_index do |localization,i|
    yield localization,i
  end
end

#each_q_frameshift ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 174

def each_q_frameshift
  @q_frameshift.each do |qfs|
    yield qfs
  end
end

#each_snp ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 134

def each_snp
  @snps.each do |snp|
    yield snp
  end
end

#each_snp_with_index ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 140

def each_snp_with_index
  @snps.each_with_index do |snp,i|
    yield snp,i
  end
end

#each_stop ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 73

def each_stop
  @stops.each do |stop|
    yield stop
  end
end

#each_stop_with_index ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 79

def each_stop_with_index
  @stops.each_with_index do |stop,i|
    yield stop,i
  end
end

#exon_acumulative ⇒ Object

Suma la longitud de todos los exones



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# File 'lib/gene_assembler/contig.rb', line 263

def exon_acumulative #Suma la longitud de todos los exones

  long=0
  exones=exones_q
  exones.each do |ex|
    long+=ex
  end
  return long
end

#exones_q ⇒ Object

Devuelve un array con el tamaño de cada hsp/exon a nivel del query



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# File 'lib/gene_assembler/contig.rb', line 229

def exones_q # Devuelve un array con el tamaño de cada hsp/exon a nivel del query

  exones_q=[]
  each_hit {|hit|
    hit.each_hsp{|hsp|
      long=(hsp.q_end-hsp.q_beg).abs
      exones_q << long
    }
  }
  return exones_q
end

#exones_s ⇒ Object

Devuelve un array con el tamaño de cada hsp/exon a nivel del subject



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# File 'lib/gene_assembler/contig.rb', line 218

def exones_s # Devuelve un array con el tamaño de cada hsp/exon a nivel del subject

  exones_s=[]
  each_hit {|hit|
    hit.each_hsp{|hsp|
      long=(hsp.s_end-hsp.s_beg).abs
      exones_s << long
    }
  }
  return exones_s
end

#first_hit ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 32

def first_hit
  h=nil
  each_hit{|hit|
     h=hit
     break
  }
  return h
end

#frameshift_modified_coordenates(add) ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 168

def frameshift_modified_coordenates(add)
  @q_frameshift.length.times do |n|
    @q_frameshift[n]+=add
  end  
end

#gff(id, parent, add) ⇒ Object

Devuelve en estrutura gff los exones en genomico



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# File 'lib/gene_assembler/contig.rb', line 571

def gff(id,parent,add) #Devuelve en estrutura gff los exones en genomico

  text=[]
  #Exones

  first_hit.each_hsp{|hsp|
#     if hsp.reversed==TRUE

#       [email protected]_beg

#       [email protected]_end

#     end

    #puts "#{hsp.q_beg+add} #{hsp.q_end+add}"

    text<<"#{id}\t.\texon\t#{hsp.q_beg+add}\t#{hsp.q_end+add}\t.\t+\t.\tID=#{parent}_exon;Parent=#{parent};Name=#{parent}_exon"
  }
  return text
end

#gff_prot(id, prot_name) ⇒ Object

Devuelve en estrutura gff los exones en proteina



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# File 'lib/gene_assembler/contig.rb', line 585

def gff_prot(id,prot_name) #Devuelve en estrutura gff los exones en proteina

  #parent="#{parent}_mRNA"

  text=[]
  #Exones

  first_hit.each_hsp{|hsp|
    #puts "#{hsp.q_beg+add} #{hsp.q_end+add}"

    text<<"#{id}\t.\tprotein_match\t#{hsp.s_beg}\t#{hsp.s_end}\t.\t+\t.\tID=#{prot_name}_prot;Parent=#{prot_name};Name=#{id}_prot"
  }
  return text
end

#has_hit? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/gene_assembler/contig.rb', line 109

def has_hit?
  has_hit=FALSE
  if @hits.length>0
    has_hit=TRUE
  end
  return has_hit
end

#hit_count ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 49

def hit_count
  count=0
  each_hit{|hit|
    count+=1
  }
  return count
end

#hits_sort! ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 146

def hits_sort!
  each_hit{|hit|
    hit.hsps_sort!  
  }
end

#hsp_at(position) ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 623

def hsp_at(position)
  hsp_ret=nil
  count_hsp=0
  found=FALSE
  each_hit {|hit|
    hit.each_hsp {|hsp|
      if position==count_hsp
        hsp_ret=hsp
        found=TRUE
        break
      end
      count_hsp+=1
    }
    if found
      break
    end  
  }
  return hsp_ret
end

#hsp_minor_than?(hsp_length) ⇒ Boolean

En nt

Returns:

  • (Boolean) 


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# File 'lib/gene_assembler/contig.rb', line 337

def hsp_minor_than?(hsp_length) # En nt

  minor=FALSE
  each_hit_with_index {|hit,i|
    if i>0 || i<hit.hsp_count
      if hit.hsp_minor_than?(hsp_length)
        minor=TRUE
        break
      end
    end
  }
  return minor
end

#indices ⇒ Object

Muestra los indices de subject y query del contig



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# File 'lib/gene_assembler/contig.rb', line 210

def indices #Muestra los indices de subject y query del contig

  each_hit_with_index {|hit,ind|
    hit.each_hsp_with_index{|hsp,i| 
      puts "#{ind+1}.#{i+1})\t#{hsp.q_beg}\t#{hsp.q_end}\t#{hsp.s_beg}\t#{hsp.s_end}\t#{@name}\t#{@length}\t#{@mod_coord}"
    }
  }
end

#intrones_q ⇒ Object

Devuelve un array con el tamaño de cada intron a nivel del query



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# File 'lib/gene_assembler/contig.rb', line 240

def intrones_q # Devuelve un array con el tamaño de cada intron a nivel del query

  intrones_q=[]
  l=first_hit.hsp_count
  each_hit {|hit|
    hit.each_hsp_with_index{|hsp,ind|
      if !first_hit.hsp_at(ind+1)
        break
      end
      long=(first_hit.hsp_at(ind+1).q_beg-hsp.q_end).abs
      intrones_q << long
    }
  }
  return intrones_q
end

#is_gapped? ⇒ Boolean

Examina si hay gaps internos en la estructura del gen q se mapea sobre la proteina q pudieran señalar la falta parcial o completa de un exon

Returns:

  • (Boolean) 


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# File 'lib/gene_assembler/contig.rb', line 304

def is_gapped? #Examina si hay gaps internos en la estructura del gen q se mapea sobre la proteina q pudieran señalar la falta parcial o completa de un exon

  gap=3 #Gap maximo permitido medido en aa, como minimo poner a 1

  gapped=FALSE
  s_end_last=0
  @hits.first.hsps.each do |hsp|
    if s_end_last >0
      dif=hsp.s_beg-s_end_last
      if dif>gap #En caso de coordenadas solapantes, siempre saldra dif negativo, con lo que la condicion gap no se cumple

        gapped=TRUE
        break
      end
    end
    s_end_last=hsp.s_end
  end
  return gapped
end

#is_one_hsp? ⇒ Boolean

Examina si el hit esta compuesto por un solo hsp

Returns:

  • (Boolean) 


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# File 'lib/gene_assembler/contig.rb', line 296

def is_one_hsp? #Examina si el hit esta compuesto por un solo hsp

  is_one=FALSE
  if first_hit.hsp_count==1
    is_one=TRUE
  end
  return is_one
end

#is_truncated? ⇒ Boolean

Examina si los exones en el borde del contig estan truncados/interrumpidos

Returns:

  • (Boolean) 


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# File 'lib/gene_assembler/contig.rb', line 321

def is_truncated? #Examina si los exones en el borde del contig estan truncados/interrumpidos

  truncated=FALSE
#   puts self.name

#   puts @hits.inspect

  #Truncado por el inicio

  if first_hit.first_hsp.s_beg>1 && first_hit.first_hsp.q_beg==1
    truncated=TRUE
  end  
  
  #Truncado por el final

  if first_hit.last_hsp.q_end==@length
    truncated=TRUE
  end  
  return truncated
end

#last_hit ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 41

def last_hit
  h=nil
  each_hit{|hit|
     h=hit
  }
  return h
end

#mixed? ⇒ Boolean

Funciones para comprobar validez de los contig

Returns:

  • (Boolean) 


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# File 'lib/gene_assembler/contig.rb', line 273

def mixed? #Examina si los hsp de un hit estan desordenados

  is_mix=FALSE
  beg=nil
  sign=0
  sign_local=0
  @hits.first.hsps.each_with_index do |hsp,c|
    if !beg.nil?
      dif=hsp.q_beg-beg
      if dif>=0
        sign_local=1
      else sign_local=0
      end
      if sign_local!=sign && c>1
        is_mix=TRUE
        break
      end
    end
    sign=sign_local
    beg=hsp.q_beg
  end
  return is_mix
end

#modified_coordenates(add) ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 152

def modified_coordenates(add)
  @mod_coord=TRUE
  each_hit{|hit|
    hit.modified_coordenates(add)
    stop_modified_coordenates(add)
    frameshift_modified_coordenates(add)
  }
  return last_hit.last_hsp.q_end
end

#n_hits? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/gene_assembler/contig.rb', line 129

def n_hits?
  n=@hits.length
  return n
end

#n_intron ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 255

def n_intron
  n_intron=0
  each_hit{|hit|
     n_intron+=1  
  }
  return n_intron
end

#overlap ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 606

def overlap
  overlap=[]
  last_hit=nil
  each_hit_with_index{|hit,i|
    overlap << hit.hsp_overlap
    if i>0
      diference=hit.overlap_with(last_hit)
      if diference<0
        overlap << diference
      end
    end
    last_hit=hit
    }
  overlap.flatten!
  return overlap
end

#rev_comp ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 407

def rev_comp
  rev_seq=[]
    @seq.each_char do |char|
      char.upcase!
      if char =='A'
        rev_seq << 'T'
      elsif char =='T'
        rev_seq << 'A'
      elsif char =='G'
        rev_seq << 'C'
      elsif char =='C'
        rev_seq << 'G'
      else
        rev_seq << char
      end
    end
    rev_seq.reverse!
    @seq=rev_seq.join
    
end

#rev_comp_if_hit ⇒ Object

Devuelve la secuencia reversocomplementaria del contig



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# File 'lib/gene_assembler/contig.rb', line 400

def rev_comp_if_hit #Devuelve la secuencia reversocomplementaria del contig

  if first_hit.reversed
    rev_comp
    first_hit.reversed=FALSE
  end
end

#rev_coord ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 428

def rev_coord
  each_hit {|hit|
    hit.rev_coord(@length)
    hit.hsps_sort!
  }
end

#start_codon_search ⇒ Object

Busqueda codon inicio, busca si existe y una vez encontrado modifica coordenadas para acomodar el codon



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# File 'lib/gene_assembler/contig.rb', line 435

def start_codon_search #Busqueda codon inicio, busca si existe y una vez encontrado modifica coordenadas para acomodar el codon

  exists=FALSE
  s_beg=@hits.first.hsps.first.s_beg
  s_end=@hits.first.hsps.first.s_end
  q_beg=@hits.first.hsps.first.q_beg
  q_end=@hits.first.hsps.first.q_end
  if s_beg<=10 # Se busca codon si la proteina carece de los 10 primeros aa

    continue=TRUE
    index=0
    temp_index=0
    while continue==TRUE 
      if temp_index==0 
        find=@seq.index('ATG')
      else
        find=@seq.index('ATG',temp_index+1)
      end  
      find+=1
      if find==nil
        continue=FALSE
      else
        if find==q_beg
          continue=FALSE
          index=find           
        elsif find>(q_beg-1+3)
          continue=FALSE
        else
          if (find-q_end).modulo(3)==0 || find-q_end==0
            index=find
          end
          if temp_index==0
            temp_index=find+1
          else
            temp_index=find
          end
        end
      end
    end#While

    if index>0
      @hits.first.hsps.first.s_beg=1
      @hits.first.hsps.first.q_beg=index
      exists=TRUE
    end
  end
  return exists
end

#stop_codon(codon, ends, *beg) ⇒ Object

Busqueda posibles codones de parada



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# File 'lib/gene_assembler/contig.rb', line 481

def stop_codon(codon,ends,*beg) #Busqueda posibles codones de parada

  reference=ends-1
  if !beg.empty?
    reference=ends
    ends=beg.first
  end
  position=nil
  follow=TRUE
  while follow
    pos=@seq.index(codon,ends)#Implicitamente lleva el +1

    if pos.nil?
      follow=FALSE
    else
      dif=(pos-reference).abs
      #puts "#{pos} #{dif} #{reference}"

      if dif.modulo(3)==0
        position=pos
        follow=FALSE
      else
        ends=pos+1
      end
    end
  end
  return position
end

#stop_codon_search ⇒ Object

Busqueda codon de parada, busca si existe



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# File 'lib/gene_assembler/contig.rb', line 523

def stop_codon_search #Busqueda codon de parada, busca si existe

  exists=FALSE
  homology_start=first_hit.first_hsp.q_beg
  homology_end=first_hit.last_hsp.q_end
  n=1
  codon=''
  position=nil
  intrones=coor_intrones
  @seq.chars do |c|
    if n<homology_start#Comenzar comparacion al principio del primer exon

      n+=1
      next
    end
    if n>homology_end#Terminar comparacion

      break
    end
    #Saltar intrones

    if !intrones.empty?
      jump=FALSE
      intrones.each do |int|
        if n>int[0] && n<int[1] #NO se incluye el borde del exon

          #print 'i'

          jump=TRUE
          break
        end
      end
      if jump
        n+=1
        next
      end
    end
    #-----------------

    codon+=c
    if codon.length==3 #Comparacion del codon

      #puts position.to_s+"\t"+codon

      if codon=='TAG'||codon=='TAA'||codon=='TGA'
        @stops << position
        exists=TRUE
      end
      codon=''
    elsif codon.length==1 #Guardar posicion del primer nucleotido del codon

      position=n
    end
    n+=1
  end
  return exists
end

#stop_modified_coordenates(add) ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 162

def stop_modified_coordenates(add)
  @stops.length.times do |n|
    @stops[n]+=add
  end  
end

#transfer_contig_hits(contig) ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 596

def transfer_contig_hits(contig)
  contig.each_hit{|hit|
    self.transfer_hit(hit)
  }
end

#transfer_hit(hit) ⇒ Object 



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# File 'lib/gene_assembler/contig.rb', line 602

def transfer_hit(hit)
  @hits << hit
end