Class: String

Inherits:
Object
  • Object
show all
Defined in:
lib/full_lengther_next/classes/lcs.rb,
lib/full_lengther_next/classes/fl_string_utils.rb

Instance Method Summary collapse

Instance Method Details

#complementary_dna ⇒ Object 



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# File 'lib/full_lengther_next/classes/fl_string_utils.rb', line 134

def complementary_dna
    c={'A'=>'T', 'a' => 't', 'T' => 'A', 't' => 'a', 'C' => 'G', 'c'=>'g' , 'G' => 'C', 'g' => 'c', 'N' => 'N', 'n' => 'N' , 'R' => 'N', 'r' => 'N', 'W' => 'N', 'w' => 'N', 'M' => 'N', 'm' => 'N', 'K' => 'N', 'k' => 'N', 'S' => 'N', 's' => 'N', 'Y' => 'N', 'y' => 'N', 'H' => 'N', 'h' => 'N', 'B' => 'N', 'b' => 'N', 'D' => 'N', 'd' => 'N', 'V' => 'N', 'v' => 'N' }
    return self.reverse.split('').map{|e| c[e]}.join
end

#generate_orf_old(a, frame) ⇒ Object 



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# File 'lib/full_lengther_next/classes/fl_string_utils.rb', line 45

def generate_orf_old(a,frame)
	
	all_orfs = []
	each_orf = []
	
	atg_codon = false
	stop_codon = false
	orf =''
	t_start = 0
	t_end = 0
	
	a.each do |e|
		t_end += 3
		if (atg_codon)
			orf += e
			if (e == 'TAG') or (e == 'TGA') or (e == 'TAA')
				if (orf.length >= 200)
					each_orf.push orf
					each_orf.push t_start
					each_orf.push t_end
					each_orf.push frame
					each_orf.push stop_codon
					
					all_orfs.push each_orf
					each_orf = []
				end
				orf=''
				stop_codon = true
				atg_codon = false
				t_start = t_end
			end
		elsif (e == 'ATG')
			atg_codon = true
			orf += e
			t_start += 1
		elsif (e == 'TAG') or (e == 'TGA') or (e == 'TAA')
			stop_codon = true
			t_start += 3
		else
			t_start += 3
		end
	end
	
	if (all_orfs != '') && (all_orfs != nil)
		return all_orfs
	else
		return nil
	end
end

#lcs(s2) ⇒ Object 



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# File 'lib/full_lengther_next/classes/lcs.rb', line 5

def lcs(s2)
	s1=self
	res="" 
	num=Array.new(s1.size){Array.new(s2.size)}
	len,ans=0
	lastsub=0
	s1.scan(/./).each_with_index do |l1,i |
		s2.scan(/./).each_with_index do |l2,j |
		  unless l1==l2
		    num[i][j]=0
		  else
		    (i==0 || j==0)? num[i][j]=1 : num[i][j]=1 + num[i-1][j-1]
		    if num[i][j] > len
		      len = ans = num[i][j]
		      thissub = i
		      thissub -= num[i-1][j-1] unless num[i-1][j-1].nil?  
		      if lastsub==thissub
		        res+=s1[i,1]
		      else
		        lastsub=thissub
		        res=s1[lastsub, (i+1)-lastsub]
		      end
		    end
		  end
		end
	end
	res
end

#orf_finder_old ⇒ Object 



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# File 'lib/full_lengther_next/classes/fl_string_utils.rb', line 95

def orf_finder_old
	res =[]
	
	s = self.upcase
	f1 = s.split('').each_slice(3).map{|e| e.join}
	r1 = generate_orf(f1,1)
	res += r1
	
	s.sub!(/^./,'')
	f2 = s.split('').each_slice(3).map{|e| e.join}
	r2 = generate_orf(f2,2)
	res += r2
	
	s.sub!(/^./,'')
	f3 = s.split('').each_slice(3).map{|e| e.join}
	r3 = generate_orf(f3,3)
	res += r3
	
	# vamos a por los ORFs de la cadena complementaria
	s = self.upcase
	s = s.complementary_dna
	
	f4 = s.split('').each_slice(3).map{|e| e.join}
	r4 = generate_orf(f4,-1)
	res += r4
	
	s.sub!(/^./,'')
	f5 = s.split('').each_slice(3).map{|e| e.join}
	r5 = generate_orf(f5,-2)
	res += r5
	
	s.sub!(/^./,'')
	f6 = s.split('').each_slice(3).map{|e| e.join}
	r6 = generate_orf(f6,-3)
	res += r6
	
	return res
end

#translate ⇒ Object 



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# File 'lib/full_lengther_next/classes/fl_string_utils.rb', line 4

def translate
	s = self.upcase
	a = s.split('').each_slice(3).map{|e| e.join}
	
    c={'GCT'=>'A', 'GCC'=>'A','GCA'=>'A','GCG'=>'A',
		'CGT'=>'R','CGC'=>'R','CGA'=>'R','CGG'=>'R','AGA'=>'R','AGG'=>'R',
		'AAT'=>'N','AAC'=>'N',
		'GAT'=>'D','GAC'=>'D',
		'TGT'=>'C','TGC'=>'C',
		'CAA'=>'Q','CAG'=>'Q',
		'GAA'=>'E','GAG'=>'E',
		'GGT'=>'G','GGC'=>'G','GGA'=>'G','GGG'=>'G',
		'CAT'=>'H','CAC'=>'H',
		'ATT'=>'I','ATC'=>'I','ATA'=>'I',
		'TTA'=>'L','TTG'=>'L','CTT'=>'L','CTC'=>'L','CTA'=>'L','CTG'=>'L',
		'ATG'=>'M',
		'AAA'=>'K','AAG'=>'K',
		'TTT'=>'F','TTC'=>'F',
		'CCT'=>'P','CCC'=>'P','CCA'=>'P','CCG'=>'P',
		'TCT'=>'S','TCC'=>'S','TCA'=>'S','TCG'=>'S','AGT'=>'S','AGC'=>'S',
		'ACT'=>'T','ACC'=>'T','ACA'=>'T','ACG'=>'T',
		'TGG'=>'W',
		'TAT'=>'Y','TAC'=>'Y',
		'GTT'=>'V','GTC'=>'V','GTA'=>'V','GTG'=>'V',
		'TAG'=>'*','TGA'=>'*','TAA'=>'*'}
	
	#EN CASO DE NO ENCONTRAR EL TRIPLETE SE AÑADE UNA X
	
	res=a.map{
		|e|
		if (e.length == 3)
			if (e =~ /[NnRrWwMmKkSsYyHhBbDdVv]/)
				'x'
			else
				c[e]||'x'
			end
		end
	}
	return res.compact.join
end