Module: CommonFunctions

Defined in:
lib/full_lengther_next/common_functions.rb

Instance Method Summary collapse

Instance Method Details

#check_frame_shift(hit) ⇒ Object 



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# File 'lib/full_lengther_next/common_functions.rb', line 130

def check_frame_shift(hit)
	fs = 0
	prot_length_in_nts = hit.q_end-hit.q_beg+1
	fs = prot_length_in_nts%3
	return fs
end

#contenidos_en_prot(key_seq, full_prot) ⇒ Object 



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# File 'lib/full_lengther_next/common_functions.rb', line 4

def contenidos_en_prot(key_seq, full_prot)	 
	full_prot = full_prot.gsub(/[\-Xx]/,'-')
	compare_prot = key_seq.gsub(/[\-Xx]/,'-')
	q_index_start = full_prot.index(compare_prot) #Full match between hit.q_seq and full_prot (unigene)
	if q_index_start.nil? #There is gaps that unables the full match
		q_index_start = match_with_ungapped_reference(full_prot, compare_prot)
		if q_index_start.nil? && full_prot.include?('-')
			diff = full_prot.length - compare_prot.length
			if scan_sequences(full_prot.split(''), compare_prot.split('')) == compare_prot.length
				q_index_start = 0
			end

			if diff >0 && scan_sequences(full_prot.split(''), compare_prot.split(''), diff) == compare_prot.length
				q_index_start = diff
			end

			if q_index_start.nil?	
				q_index_start = match_with_gapped_reference(full_prot, compare_prot)
			end
		end
		if q_index_start.nil?
			q_index_start = 0
		end

	end
	return q_index_start
end

#corrige_frame(ref_frame, ref_start, ref_end) ⇒ Object 



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# File 'lib/full_lengther_next/common_functions.rb', line 116

def corrige_frame(ref_frame,ref_start,ref_end)

	if (ref_frame.abs == 2)
		ref_start = ref_start + 1
		ref_end = ref_end + 1
	elsif (ref_frame.abs == 3)
		ref_start = ref_start + 2
		ref_end = ref_end + 2
	end
	
	return [ref_start,ref_end]

end

#extend_match(full_prot, compare_prot, q_index_start, compare_prot_index) ⇒ Object 



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# File 'lib/full_lengther_next/common_functions.rb', line 55

def extend_match(full_prot, compare_prot, q_index_start, compare_prot_index)
	full_prot_substring = full_prot[0..q_index_start-1].reverse.split('')
	compare_prot_substring = compare_prot[0..compare_prot_index-1].reverse.split('')
	extend_match = scan_sequences(full_prot_substring, compare_prot_substring)
	q_index_start -= extend_match
	compare_prot_index -= extend_match
	return q_index_start, compare_prot_index
end

#match_with_gapped_reference(full_prot, compare_prot) ⇒ Object 



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# File 'lib/full_lengther_next/common_functions.rb', line 33

def match_with_gapped_reference(full_prot, compare_prot)
	q_index_start = nil
	fragments_array = full_prot.split(/\-+/)
	fragments_array.each_with_index do |seq, i|
		if seq.length > 4
			compare_prot_index = compare_prot.index(seq)
			if compare_prot_index.nil? # In cases that no match by gaps
				seq =seq[0..4]
				compare_prot_index = compare_prot.index(seq)
			end
			if !compare_prot_index.nil?
				q_index_start = full_prot.index(seq)
				if i > 0
					q_index_start, compare_prot_index = extend_match(full_prot, compare_prot, q_index_start, compare_prot_index)
				end
				break
			end
		end			
	end
	return q_index_start
end

#match_with_ungapped_reference(full_prot, compare_prot) ⇒ Object 



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# File 'lib/full_lengther_next/common_functions.rb', line 78

def match_with_ungapped_reference(full_prot, compare_prot)
	q_index_start = nil
	fragments_array = compare_prot.split(/\-+/)
	fragments_array.each_with_index do |seq, i|
		if q_index_start.nil? && seq.length > 4
			q_index_start = full_prot.index(seq)
			if i > 0 && !q_index_start.nil?
				q_index_start = refine_match(seq, compare_prot, q_index_start) # Correction if first seq isn't enough large
			end
			break
		end
	end
	return q_index_start
end

#refine_match(subseq, seq, q_index_start) ⇒ Object 



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# File 'lib/full_lengther_next/common_functions.rb', line 93

def refine_match(subseq, seq, q_index_start)
	location_seq = seq.index(subseq)
	gaps_on_location = seq[0..location_seq].count('-')
	q_index_start -=  location_seq - gaps_on_location # Correction if first seq isn't enough large 
	return q_index_start
end

#reverse_seq(query_fasta, hit) ⇒ Object 



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

def reverse_seq(query_fasta, hit)
	hit.q_frame = -hit.q_frame
	hit.q_end = query_fasta.length - 1 - hit.q_end 	
	hit.q_beg = query_fasta.length - 1 - hit.q_beg
	hit.reversed = true
	query_fasta = query_fasta.complementary_dna # ESTO REALMENTE HACE LA REVERSO COMPLEMENTARIA.
	if hit.class.to_s == 'ExoBlastHit'
		hit.q_frameshift.map!{|position, num_nts|
			reversed_position = query_fasta.length - 1 - position  
			[reversed_position, num_nts]
		}
	end
	return query_fasta
end

#scan_sequences(ref_seq, compare_seq, diff = 0) ⇒ Object 



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# File 'lib/full_lengther_next/common_functions.rb', line 64

def scan_sequences(ref_seq, compare_seq, diff = 0)
	extend_match = 0
	ref_seq.each_with_index do |char,i|
		if i >= diff
			compare_char = compare_seq[extend_match]
			if compare_char.nil? || char != compare_char && char != '-' && compare_char != '-' 
				break
			end
			extend_match += 1
		end
	end
	return extend_match
end