Class: Sequence

Inherits:
Object
  • Object
show all
Defined in:
lib/full_lengther_next/classes/sequence.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(seq_name, seq_fasta, seq_qual = '') ⇒ Sequence

Returns a new instance of Sequence.



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# File 'lib/full_lengther_next/classes/sequence.rb', line 8

def initialize(seq_name,seq_fasta,seq_qual='')
	fasta_ori = seq_fasta.dup
	@seq_name=seq_name
	@seq_fasta = seq_fasta
	@fasta_length = fasta_ori.length
	change_degenerated_nt!
	@seq_qual = ''
	@sec_desc = ''
	@annotations=[]
	@orfs=[]
	
	@rejected=false
	@rejected_message=''
	
end

Instance Attribute Details

#fasta_length ⇒ Object

Returns the value of attribute fasta_length.



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# File 'lib/full_lengther_next/classes/sequence.rb', line 6

def fasta_length
  @fasta_length
end

#orfs ⇒ Object

Returns the value of attribute orfs.



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# File 'lib/full_lengther_next/classes/sequence.rb', line 6

def orfs
  @orfs
end

#sec_desc ⇒ Object

Returns the value of attribute sec_desc.



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# File 'lib/full_lengther_next/classes/sequence.rb', line 6

def sec_desc
  @sec_desc
end

#seq_fasta ⇒ Object

Returns the value of attribute seq_fasta.



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# File 'lib/full_lengther_next/classes/sequence.rb', line 6

def seq_fasta
  @seq_fasta
end

#seq_name ⇒ Object

Returns the value of attribute seq_name.



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# File 'lib/full_lengther_next/classes/sequence.rb', line 6

def seq_name
  @seq_name
end

#seq_qual ⇒ Object

Returns the value of attribute seq_qual.



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# File 'lib/full_lengther_next/classes/sequence.rb', line 6

def seq_qual
  @seq_qual
end

Instance Method Details

#add_orf(orf_seq, orf_t_start, orf_t_end, orf_frame, orf_stop_codon, orf_type) ⇒ Object 



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# File 'lib/full_lengther_next/classes/sequence.rb', line 24

def add_orf(orf_seq, orf_t_start, orf_t_end, orf_frame, orf_stop_codon, orf_type)
	orf = Orf.new(orf_seq, orf_t_start, orf_t_end, orf_frame, orf_stop_codon, orf_type)
	@orfs.push orf
	
end

#annotate(annotation_type, message = '', replace_existing = false) ⇒ Object 



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# File 'lib/full_lengther_next/classes/sequence.rb', line 44

def annotate(annotation_type, message='', replace_existing = false)

	if replace_existing
		@annotations.reverse_each do |annotation| 
			if annotation[:annotation_type]==annotation_type
				@annotations.delete(annotation)
			end
		end
	end
	
	
	@annotations.push({:annotation_type=>annotation_type,:message=>message})
end

#change_degenerated_nt! ⇒ Object 



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# File 'lib/full_lengther_next/classes/sequence.rb', line 58

def change_degenerated_nt!
	
	
	########################################

	tranlaste_hash = {}
	tranlaste_hash['R']= [['a','g'],0]
	tranlaste_hash['W']= [['a','t'],0]
	tranlaste_hash['M']= [['a','c'],0]
	tranlaste_hash['K']= [['g','t'],0]
	tranlaste_hash['S']= [['g','c'],0]
	tranlaste_hash['Y']= [['c','t'],0]
	tranlaste_hash['H']= [['a','t','c'],0]
	tranlaste_hash['B']= [['g','t','c'],0]
	tranlaste_hash['D']= [['g','a','t'],0]
	tranlaste_hash['V']= [['g','a','c'],0]
	tranlaste_hash['N']= [['g','a','c','t'],0]

	########################################

	fix_degenerated_fasta!(tranlaste_hash)
	
	
end

#fix_degenerated_fasta!(tranlaste_hash) ⇒ Object 



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# File 'lib/full_lengther_next/classes/sequence.rb', line 83

def fix_degenerated_fasta!(tranlaste_hash)
	s = @seq_fasta
	res = []

	nts_of_a_line = s.split('')

	nts_of_a_line.map{
		|e|
		# puts "#{e} "

		if (e =~ /[RWMKSYHBDVN]/)

			# puts "#{e} "
			tranlaste_hash[e][1] += 1
			# puts "#{e}  #{tranlaste_hash[e][1]}"

			e = tranlaste_hash[e][0][tranlaste_hash[e][1]%tranlaste_hash[e][0].length]

			# puts "#{e}"
		end

		res.push e

	}

	@seq_fasta=res.compact.join
	# @seq_fasta='dario'
end

#get_annotations(annotation_type) ⇒ Object

:complete, :tmp_annotation, :error, :protein, :nucleotide, :alignment, :tcode



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# File 'lib/full_lengther_next/classes/sequence.rb', line 40

def get_annotations(annotation_type)
	return @annotations.select{|a| a[:annotation_type]==annotation_type}
end

#reject!(message = '') ⇒ Object 



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# File 'lib/full_lengther_next/classes/sequence.rb', line 34

def reject!(message='')
	@rejected=true
	@rejected_message=message
end

#rejected? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/full_lengther_next/classes/sequence.rb', line 30

def rejected?
	return @rejected
end