Class: ExonerateResult

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

Overview

Extracts results from blast table’s file and uses it to create instances of “BlastQuery” and “BlastHit”

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(input, seqs = nil, query_seqs = nil, all = true) ⇒ ExonerateResult

Parser initialization



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# File 'lib/full_lengther_next/exonerate_result.rb', line 42

def initialize(input, seqs= nil, query_seqs = nil, all = true)
  @querys = []
  @seqs = seqs #unigenes
  @prot_seqs = query_seqs#prot

  if input.is_a?(Array)
  	input.each do |file|
     	parse_file(File.open(file).readlines, all)
   	end
  else
    parse_file(File.open(input).readlines, all)
  end
  query_name=''
end

Instance Attribute Details

#querys ⇒ Object

Returns the value of attribute querys.



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# File 'lib/full_lengther_next/exonerate_result.rb', line 256

def querys
  @querys
end

Instance Method Details

#convert_parsed_lines(lines_parsed) ⇒ Object 



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# File 'lib/full_lengther_next/exonerate_result.rb', line 81

def convert_parsed_lines(lines_parsed)
	last_query = nil
	query = nil
	lines_parsed.each_with_index do |line|
		begin
			if lines_parsed.class.to_s=='Array'
				align_data=line['align_data']
				features=line
			else #hash
				align_data=line[1]['align_data']
				features=line[1]        
			end
			tags = align_data.scan(/([MFG53S]) ([0-9]+) ([0-9]+)/)
			tags.map!{|tag| [tag[0], tag[1].to_i, tag[2].to_i]}
			if features['target_id'] != last_query
				last_query = features['target_id']
				query = BlastQuery.new(features['target_id'])
				@querys << query
			end
		  	hiting(features,tags, query)
		rescue
			puts "Result: #{features['target_id']} => #{features['query_id']} hasn't been parsed\n#{line}"
		end
	end    
end

#define_hit_parameters(hit, features, tags) ⇒ Object 



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# File 'lib/full_lengther_next/exonerate_result.rb', line 203

def define_hit_parameters(hit, features, tags)
	hit.gaps = 0
	tags.map{|aln| hit.gaps += 1 if aln[0] == 'G'}
	hit.reversed = false
	hit.align_len =(features['query_end_align'] - features['query_start_align']).abs+1 
	hit.mismatches=0
	hit.e_val=0
	hit.bit_score=0
	hit.score = features['score']
	hit.s_frame = nil
	strand = 1
	strand = -1 if features['target_strand'] == '-'
	hit.q_frame = (((features['target_start_align']) % 3) +1) *strand
	hit.subject_id = features['query_id']
	hit.full_subject_length=0
	hit.definition=''
	hit.acc=features['query_id']
	hit.q_seq=''
	hit.s_seq=''
end

#do_reverso_complementary(counter_target, target_seq) ⇒ Object

def



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# File 'lib/full_lengther_next/exonerate_result.rb', line 186

def do_reverso_complementary(counter_target, target_seq)
	counter_target = target_seq.length - 1 - counter_target 
	target_seq = target_seq.complementary_dna
	return counter_target, target_seq
end

#empty? ⇒ Boolean

check if there are querys

Returns:

  • (Boolean) 


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# File 'lib/full_lengther_next/exonerate_result.rb', line 246

def empty?

  return @querys.empty?
end

#find_query(querys, name_q) ⇒ Object

find query by name



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# File 'lib/full_lengther_next/exonerate_result.rb', line 234

def find_query(querys,name_q)
  #  newq = querys.find{|q| ( q.find{|h| (h.subject_id)})}
  new_q=nil

  if !querys.empty?
    new_q=querys.find{|q| (q.query_id==name_q)}
  end

  return new_q
end

#hiting(features, tags, query) ⇒ Object

this method only works fine with –model protein2dna parameter of exonerate



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# File 'lib/full_lengther_next/exonerate_result.rb', line 108

def hiting(features, tags, query) #Convierte las coordenadas relativas del exonerate a absolutas tipo blast, definiendo solo los hits		
	do_align = false
	do_align = true if !@prot_seqs.nil? && !@seqs.nil?
	start_target = features['target_start_align']#Unigen
	start_query = features['query_start_align'] #proteina
	ends_target = features['target_end_align']
	ends_query = features['query_end_align']-1 # -> Exonerate don't set to 0 position the ends of target and query
	if features['target_strand'] == '-' #-> Exonerate don't set to 0 position the ends of target and query
		start_target -= 1 # Start target is end target when mathc is in reversed complementary strand
	else
		ends_target -= 1
	end
	hit = ExoBlastHit.new(start_target+1, ends_target+1, start_query+1, ends_query+1)
	define_hit_parameters(hit, features, tags)
	query.add_hit(hit)
	
	#Define alignment and blast like parameters
	target_alignment = ''
	query_alignment = ''
	counter_target = start_target
	counter_query = start_query
	if do_align #get seqs
		query_seq = @prot_seqs[features['query_id']]
		target_seq = @seqs[features['target_id']]
	end
	counter_target, target_seq = do_reverso_complementary(counter_target, target_seq) if features['target_strand'] == '-'
	query_frameshift = []
	target_frameshift = []
	gap_shift = 0
	#puts features['query_id']+ ' ' +features['target_strand'], '-----------------------'
	tags.each_with_index do |tag, n_operation|
		#puts tag.inspect
		if do_align
			gap_shift = 0 if tag[OPERATION] != 'G'
			query_alignment << query_seq[counter_query, tag[QUERY]]
			target_alignment << target_seq[counter_target, tag[TARGET]].translate
		end
		if tag[OPERATION] == 'F'
			if tag[TARGET] > 0 && tag[TARGET] < 3 #true FRAMESHIFT
				gap_shift += 1
				if tags[n_operation+1][OPERATION] != 'G' #there are frameshift that not insert a gap, we do it
					query_alignment <<  '-' if do_align
				end
			else
				query_alignment <<  '-' * (tag[TARGET]/3.0).ceil if do_align
			end
			query_frameshift << counter_query
			fs_counter_target = counter_target
			fs_counter_target = target_seq.length - counter_target if features['target_strand'] == '-' # ESto es un apaño, habria que plantear el parseo de las reversas como reduccion en el contador del formato del exonerate, en vez de como adiccion
			if tag[TARGET] > 3
				real_fs = tag[TARGET]%3
				real_gap = tag[TARGET] - real_fs
				fs = [fs_counter_target + real_gap, real_fs]
			else
				fs = [fs_counter_target, tag[TARGET]]
			end
			target_frameshift << fs
		elsif tag[OPERATION] == 'G'
			query_alignment <<  '-' * (tag[TARGET]/3.0).ceil if do_align
			diff = tag[QUERY] - gap_shift
			target_alignment << '-' * diff if do_align && diff > 0
			gap_shift = 0
		end	
		counter_query += tag[QUERY]
		counter_target += tag[TARGET]
	end
	hit.s_frameshift = query_frameshift
	hit.q_frameshift = target_frameshift

	#puts "\e[33m#{target_alignment}\e[0m", "\e[36m#{query_alignment}\e[0m"
	if do_align
		hit.q_seq = target_alignment
		hit.s_seq = query_alignment
		hit.align_len = query_alignment.length
		hit.ident = set_ident(target_alignment,query_alignment)
	end
end

#inspect ⇒ Object

inspect results



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

def inspect
  res = "Exonerate results:\n"
  res+= '-'*20
  res+= "\nQuerys: #{@querys.count}\n"
  @querys.each{|q| res+=q.inspect+"\n"}
  return res
end

#parse_file(lines, all) ⇒ Object 



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# File 'lib/full_lengther_next/exonerate_result.rb', line 57

def parse_file(lines, all)
	lines_parsed=[] 
  lines_parsed={} if !all
  lines.each do |line|
if line=~ /^vulgar:/
	line.chomp!
	fields=line.split(' ', 11)
	features={'query_id'=> fields[1], 'query_start_align'=> fields[2].to_i, 'query_end_align'=> fields[3].to_i, 'query_strand'=> fields[4],'target_id'=> fields[5], 'target_start_align'=> fields[6].to_i, 'target_end_align'=> fields[7].to_i, 'target_strand'=> fields[8], 'score'=> fields[9].to_i, 'align_data'=> fields[10]}
	if all
		lines_parsed << features
	else
	  if !lines_parsed.key?(features['target_id']) # Añadir valor si no existe
	    lines_parsed[features['target_id']]=features
	  else
	    if features['score']>lines_parsed[features['target_id']]['score'] # Si ya existe una query, ver si la nueva presenta un mayor score y reemplazar la antigua
	    	lines_parsed[features['target_id']]=features
	    end
	  end
	end
end
		end		
		convert_parsed_lines(lines_parsed)	
end

#set_ident(target_alignment, query_alignment) ⇒ Object 



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# File 'lib/full_lengther_next/exonerate_result.rb', line 192

def set_ident(target_alignment, query_alignment)
	matchs = 0
	position = 0
	target_alignment.each_char do |char|
		matchs +=1 if char == query_alignment[position]
		position +=1
	end
	perc_ident = ('%.2f' % (matchs*100.0/target_alignment.length)).to_f
	return perc_ident
end

#size ⇒ Object

get query count



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# File 'lib/full_lengther_next/exonerate_result.rb', line 252

def size
  @querys.size
end