Class: Sequence

Inherits:
Object
  • Object
show all
Defined in:
lib/full_lengther_next/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/sequence.rb', line 10

def initialize(seq_name, seq_fasta, seq_qual='')
	@seq_name = seq_name
	@seq_fasta = seq_fasta
	@fasta_length = seq_fasta.length
	@db_name = nil
	@seq_nt = nil # Unigen sequence with tagged ATG & stop
	@seq_aa = nil # Protein sequence generated over unigen
	@db =nil
	@type = UNKNOWN # See types.rb
	@status = false # true => Sure, false => Putative
	@id = nil #Prot or EST id, can be several => array
	@warnings = []
	@annotations=[]
	@functional_annotations = {}
	@orfs=[]

	#Mapping_info
	@fpkm = []
	@coverage_analysis = []
	
	@area_without_annotation=false
	@save_fasta=true
	@ignore = false 
	@hit=nil
	@t_code=0
end

Instance Attribute Details

#area_without_annotation ⇒ Object

Returns the value of attribute area_without_annotation.



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

def area_without_annotation
  @area_without_annotation
end

#coverage_analysis ⇒ Object

Returns the value of attribute coverage_analysis.



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

def coverage_analysis
  @coverage_analysis
end

#db ⇒ Object

Returns the value of attribute db.



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

def db
  @db
end

#db_name ⇒ Object

Returns the value of attribute db_name.



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

def db_name
  @db_name
end

#fasta_length ⇒ Object

Returns the value of attribute fasta_length.



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

def fasta_length
  @fasta_length
end

#fpkm ⇒ Object

Returns the value of attribute fpkm.



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

def fpkm
  @fpkm
end

#functional_annotations ⇒ Object

Returns the value of attribute functional_annotations.



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

def functional_annotations
  @functional_annotations
end

#hit ⇒ Object

Returns the value of attribute hit.



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

def hit
  @hit
end

#id ⇒ Object

Returns the value of attribute id.



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

def id
  @id
end

#ignore ⇒ Object

Returns the value of attribute ignore.



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

def ignore
  @ignore
end

#orfs ⇒ Object

Returns the value of attribute orfs.



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

def orfs
  @orfs
end

#save_fasta ⇒ Object

Returns the value of attribute save_fasta.



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

def save_fasta
  @save_fasta
end

#seq_aa ⇒ Object

Returns the value of attribute seq_aa.



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

def seq_aa
  @seq_aa
end

#seq_fasta ⇒ Object

Returns the value of attribute seq_fasta.



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

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/sequence.rb', line 8

def seq_name
  @seq_name
end

#seq_nt ⇒ Object

Returns the value of attribute seq_nt.



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

def seq_nt
  @seq_nt
end

#status ⇒ Object

Returns the value of attribute status.



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

def status
  @status
end

#t_code ⇒ Object

Returns the value of attribute t_code.



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

def t_code
  @t_code
end

#type ⇒ Object

Returns the value of attribute type.



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

def type
  @type
end

Instance Method Details

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



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# File 'lib/full_lengther_next/sequence.rb', line 38

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

#all_warns ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 201

def all_warns
	all = @warnings.join(' ')
	return all
end

#area_without_annotation? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/full_lengther_next/sequence.rb', line 464

def area_without_annotation?
	if @hit.class == Array
		hit = @hit.first
	else
		hit = @hit
	end
	upstream_annotation_space = hit.q_beg 
	downstream_annotation_space = @fasta_length - hit.q_end
	if upstream_annotation_space >= 150 || downstream_annotation_space >= 150
		@area_without_annotation = true
	end
	return @area_without_annotation
end

#calification ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 282

def calification
	type_description = nil
	case @type
		when FAILED
			type_description = 'Failed'
		when OTHER
			type_description = 'Other'
		when UNMAPPED
			type_description = 'Unmapped'
		when CHIMERA
			type_description = 'Chimera'
		when MISASSEMBLED
			type_description = 'Misassembled'
		when UNKNOWN
			type_description = 'Unknown'
		when COMPLETE
			type_description = 'Complete'
		when N_TERMINAL 
			type_description = 'N_terminal'
		when C_TERMINAL
			type_description = 'C_terminal'
		when INTERNAL
			type_description = 'Internal'
		when CODING
			type_description = 'Coding'
		when NCRNA
			type_description = 'NcRNA'
	end

end

#change_degenerated_nt! ⇒ Object 



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

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


	fix_degenerated_fasta!(translate_hash)		
end

#check_warn(warn) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 128

def check_warn(warn)
	check = warn
	replace = nil
	if warn.class.to_s == 'Array'
		check = warn.shift # Take warning tag message
		replace = warn # Take values to replace in message
	end

	message = $warnings_hash[check]
	if message.nil?
		message = check # If not exists the message
	end

	if !replace.nil?
		message = message.dup # Duplicate memory to avoid overwrite original warning hash messages
		replace.each do |rep|
			message.sub!('(*replace*)',"#{rep}") #message variable
		end
	end
	return message
end

#clean_annotations ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 96

def clean_annotations
	@annotations = []
end

#clean_orfs ⇒ Object 



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

def clean_orfs
	@orfs=[]
end

#clean_warnings ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 92

def clean_warnings
	@warnings = []
end

#clone ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 478

def clone
	new_seq = self.dup
	new_seq.clean_annotations
	new_seq.clean_warnings
	new_seq.clean_orfs
	new_seq.clone_warnings(@warnings)
	new_seq.clone_annotations(@annotations)
	return new_seq
end

#clone_annotations(array_annotations) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 488

def clone_annotations(array_annotations)
	array_annotations.map{|annotation| @annotations << annotation.dup}
end

#clone_warnings(array_warnings) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 124

def clone_warnings(array_warnings)
	array_warnings.map{|warn| @warnings << warn.dup}
end

#fix_degenerated_fasta!(translate_hash) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 63

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

	nts_of_a_line = s.split('')

	nts_of_a_line.map{|e|

		if (e =~ /[RWMKSYHBDVN]/)
			translate_hash[e][1] += 1
			e = translate_hash[e][0][translate_hash[e][1]%translate_hash[e][0].length]
		end

		res << e

	}

	@seq_fasta=res.compact.join
end

#format_chimera! ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 110

def format_chimera!
	@hit = []
end

#get_acc ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 100

def get_acc
	acc=hit.acc
	return acc
end

#get_fasta(seq) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 157

def get_fasta(seq)
	fasta = ">#{@seq_name}\n#{seq}"
	return fasta
end

#get_pident ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 105

def get_pident
	pident=hit.ident
	return pident
end

#print_alignment(aa_align, nt_align, color, show_nts, mark_subzone = nil) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 375

def print_alignment(aa_align, nt_align, color, show_nts, mark_subzone = nil)
	original_color = color
	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'=>'*'}
	
	nt_line = ''
	aa_line = ''
	gaps = 0
	count = 0
	aa_align.each_with_index do |aa, n|
		if aa == '-'
			nt_line << '---'
			gaps += 1
		else
			# Check aa with codon
			codon_window = (n-gaps)*3
			codon = nt_align[codon_window..codon_window+2]
			nt_line << "#{codon}"
			if aa.upcase != 'X' 
				if codon.upcase.include?('N')
					traslated_aa = '-'
				else	
					traslated_aa = c[codon]
				end
				if traslated_aa != '-' && traslated_aa != aa
					puts "#{traslated_aa} #{aa}"
					aa = '?'
				end
			end
		end
		if !mark_subzone.nil?
			nts_coordenate = (n-gaps)*3
			mark_subzone.values.each do |subzone|
				if nts_coordenate >= subzone[0] && nts_coordenate <= subzone[1] #0 => first coordenate, 1 => second coordenate
					color = subzone.last
				end
			end
		end
		space = nil
		if show_nts
			space = ' '
		end
		aa_line << "\e[#{color}m#{space}#{aa}#{space}\e[0m"
		color = original_color
		line_length = 60
		if (n+1) % line_length == 0 || n+1 == aa_align.length
			count = n + 1
			print "#{count}\t"
			puts aa_line
			if show_nts
				print "#{count*3}\t"
				puts nt_line
			end
			aa_line = ''
			nt_line = ''
		end
	end

end

#prot_annot_calification ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 313

def prot_annot_calification
	info = "#{calification} "	
	if @status
		info << 'Sure'
	else
		info << 'Putative'
	end
	return info
end

#reduce_coordinates(subzone_align, aa_align, h) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 454

def reduce_coordinates(subzone_align, aa_align, h)
	if !subzone_align.nil?
		aligned = 3 * aa_align.length + h.q_frame-1
		subzone_align.values.each do |subzone|
			subzone[0]-= aligned 
			subzone[1]-= aligned 
		end
	end
end

#reset_classification ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 87

def reset_classification
	@type = UNKNOWN
	@status = false
end

#show_alignment(h, nts, show_nts, original_query_coordinates = nil) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 323

def show_alignment(h, nts, show_nts, original_query_coordinates = nil)
	puts "Prot id:\t#{h.acc}", "Alignment length:\t#{h.align_len} aa", "Subject   length:\t#{h.s_len} aa", "Query length:\t#{nts.length/3} aa"
	puts prot_annot_calification
	puts

	aa_unigen = nts[h.q_frame - 1 .. nts.length-1].translate
	index = contenidos_en_prot(h.q_seq, aa_unigen)

	# View desplacements 5-prime/align/3-prime
	subzone_align = nil
	if !original_query_coordinates.nil?
		subzone_align = {}
		if h.q_beg > original_query_coordinates.first #alignment has transferred characters to 5 prime
			subzone_align['beg'] = [original_query_coordinates.first, h.q_beg-3, 42] # -3 to exclude the last aa
		elsif h.q_beg < original_query_coordinates.first
			subzone_align['beg'] = [h.q_beg, original_query_coordinates.first-3, 46] #alignment has received characters from 5 prime
		end

		if h.q_end < original_query_coordinates.last #alignment has transferred characters to 3 prime
			subzone_align['end'] = [h.q_end, original_query_coordinates.last, 42]
		elsif h.q_end > original_query_coordinates.last
			subzone_align['end'] = [original_query_coordinates.last, h.q_end, 43] #alignment has received characters from 3 prime
		end
	end

	# Print 5 prime
	if index > 0 # 5 prime  exists
		aa_align = aa_unigen[0 .. index-1].split('')
		nt_align = nts[h.q_frame-1..h.q_beg-1]
		print_alignment(aa_align, nt_align, 36, show_nts, subzone_align)
		reduce_coordinates(subzone_align, aa_align, h)
	end

	# Print core alignment or protein
	aa_align = h.q_seq.split('')
	nt_align = nts[h.q_beg..h.q_end]
	print_alignment(aa_align, nt_align, 32, show_nts, subzone_align)
	reduce_coordinates(subzone_align, aa_align, h)

	# Print 3 prime
	gaps = h.q_seq.count('-')
	three_prime_beg = index+h.q_seq.length-gaps
	if aa_unigen.length > three_prime_beg # 3 prime  exists
		aa_align = aa_unigen[three_prime_beg .. aa_unigen.length-1].split('')
		fs = check_frame_shift(h)
		nt_align = nts[h.q_end+1-fs..nts.length-1]
		print_alignment(aa_align, nt_align, 33, show_nts, subzone_align)
	end

end

#test_code(test_code) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 150

def test_code(test_code)
	@t_code = test_code
	if @t_code >= 0.95
		@status = true
	end
end

#unmapped? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/full_lengther_next/sequence.rb', line 492

def unmapped?
	res = false
	res = true if !@coverage_analysis.empty? && @coverage_analysis[3] == 0 #3 => percentage of sequence covered by reads 
	return res
end

#warnings(warn) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 114

def warnings(warn)
	if warn.class.to_s == 'Array'
		warn.each do |w|
			@warnings << check_warn(w)
		end
	else
		@warnings << check_warn(warn)
	end
end

#write_align(file) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 265

def write_align(file)
	tabs = (seq_name.length/8).ceil
	if tabs == 0
		tabs = 1
	end
	second_tab = 0
	if seq_name.length > 7
		second_tab = 1
	end
	file.puts "#{@seq_name}#{"\t"*tabs}#{@hit.q_seq}\n#{@hit.acc}#{"\t"*(tabs+second_tab)}#{@hit.s_seq}"
	file.puts
end

#write_chimera(file) ⇒ Object

TODO : write ‘SOLVED’ tag



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# File 'lib/full_lengther_next/sequence.rb', line 214

def write_chimera(file) #TODO : write 'SOLVED' tag
	@hit.each do |h|
		file.puts "#{@seq_name}\t#{@fasta_length}\t#{h.acc}\t#{@db_name}\t#{h.q_frame}\t#{h.e_val}\t#{h.ident}\t#{h.q_beg + 1}\t#{h.q_end + 1}\t#{h.s_beg + 1}\t#{h.s_end + 1}\t#{h.definition}"
	end
	file.puts
end

#write_coding(file) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 251

def write_coding(file)
	# ħit is an array. 2 => q_frame, 1 ORF end, 0 ORF beg 
	calification = 'Putative'
	if @status
		calification = 'Sure'
	end
	file.puts "#{@seq_name}\t#{@fasta_length}\t#{calification}\t#{@t_code}\t#{@hit.last}\t#{@hit.first}\t#{@hit[1]}"
end

#write_info(output_files) ⇒ Object

Output_files is a hash



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# File 'lib/full_lengther_next/sequence.rb', line 162

def write_info(output_files) # Output_files is a hash
	if @save_fasta
		output_files['seqs'].puts get_fasta(@seq_fasta)	
	end
	if !@fpkm.empty?
		output_files['fpkm'].puts "#{@seq_name}\t#{@fpkm.join("\t")}"
	end
	if !@coverage_analysis.empty?
		all_coverages = @coverage_analysis.last
		output_files['coverage'].puts "#{@seq_name}\t#{@coverage_analysis[0..@coverage_analysis.length-1].join("\t")}"
	end

	case @type
	when OTHER
		write_other(output_files[@type])
	when CHIMERA
		write_chimera(output_files[@type])
	when UNMAPPED
		write_unmapped(output_files[@type])
	when MISASSEMBLED
		write_misassembled(output_files[@type])
	when UNKNOWN
		write_unknown(output_files[@type])
	when COMPLETE .. INTERNAL
		write_prot_annot(output_files['db'])
		write_prot_seq(output_files['prot'])
		write_nt_seq(output_files['nts'])
		write_align(output_files['align'])
	when NCRNA
		write_ncrna(output_files[@type])
	when CODING
		write_coding(output_files[@type])
	else
		if @type != FAILED
			raise "#{@type} is an incorrect type"
		end
	end
end

#write_misassembled(file) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 221

def write_misassembled(file)
	file.puts "#{@seq_name}\t#{@fasta_length}\t#{@hit.acc}\t#{@db_name}"
end

#write_ncrna(file) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 247

def write_ncrna(file)
	file.puts "#{@seq_name}\t#{@fasta_length}\t#{@hit.acc}\t#{@hit.e_val}\t#{@hit.ident}\t#{@hit.q_beg + 1}\t#{@hit.q_end + 1}\t#{@hit.s_beg + 1}\t#{@hit.s_end + 1}\t#{@hit.definition}"
end

#write_nt_seq(file) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 278

def write_nt_seq(file)
	file.puts "#{@seq_name}\t#{@fasta_length}\t#{@seq_nt}"
end

#write_other(file) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 206

def write_other(file)
	file.puts "#{@seq_name}\t#{@fasta_length}\t#{@hit.acc}\t#{@db_name}\t#{all_warns}"
end

#write_prot_annot(file) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 239

def write_prot_annot(file)
	final_func_annot = Array.new(9, '-')
	if !@functional_annotations.empty?
		final_func_annot = @functional_annotations.values
	end
	file.puts "#{@seq_name}\t#{@fasta_length}\t#{@hit.acc}\t#{@db_name}\t#{prot_annot_calification}\t#{@hit.e_val}\t#{@hit.ident}\t#{@hit.full_subject_length}\t#{@seq_aa.length}\t#{all_warns}\t#{@hit.q_frame}\t#{@hit.q_beg + 1}\t#{@hit.q_end + 1}\t#{@hit.s_beg + 1}\t#{@hit.s_end + 1}\t#{@hit.definition}\t#{final_func_annot.join("\t")}"
end

#write_prot_seq(file) ⇒ Object

Write complementary files



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# File 'lib/full_lengther_next/sequence.rb', line 261

def write_prot_seq(file)
	file.puts get_fasta(@seq_aa)
end

#write_unknown(file) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 225

def write_unknown(file)
	# ħit is an array. 2 => q_frame, 1 ORF end, 0 ORF beg
	if hit.class.to_s == 'Array'
		orf_beg = @hit[0]
		orf_end = @hit[1]
		q_frame = @hit[2]		
	else 
		orf_beg = '-'
		orf_end = '-'
		q_frame = '-'
	end
	file.puts "#{@seq_name}\t#{@fasta_length}\t#{@t_code}\t#{all_warns}\t#{q_frame}\t#{orf_beg}\t#{orf_end}"
end

#write_unmapped(file) ⇒ Object 



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# File 'lib/full_lengther_next/sequence.rb', line 210

def write_unmapped(file)
	file.puts "#{@seq_name}\t#{@fasta_length}"
end