module CommonFunctions

Public Instance Methods

check_frame_shift(hit) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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