Created
July 31, 2014 21:16
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A short script that takes a DNA strand, does a pattern search and returns # the indexes of all matches.
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| # Author: Adam Loo | |
| # Date: 7/31/2014 | |
| # A short script that takes a DNA strand, does a pattern search and returns | |
| # the indexes of all matches. | |
| STRAND = "aggcgtatgcgatcctgaccatgcaaaactccagcgtaaatacctagccatggcgacacaaggcgcaaga" + | |
| "caggagatgacggcgtttagatcggcgaaatattaaagcaaacgacgatgacttcttcgggaaattagttccctactcgt" + | |
| "gtactccaattagccataacactgttcgtcaagatatagggggtcacccatgaatgtcctctaaccagaccatttcgtta" + | |
| "cacgaacgtatctgatgacttcttcgggaaattagttccctactcgtgtactccaattagccataacactgttcgtcaag" + | |
| "atatagggggtcacccatgaatgtcctctaaccagaccatttcgttacacgaacgtatcttcggggcgtatgcgatcctg" + | |
| "accatgcaaaactccagcgtaaatacctagccatggcgacacaaggcgcaagacaggagatgacggcgtttagatcggcg" + | |
| "aaatattaaagcaaacgacgatgacttcttcgggaaattagttccctactcgtgtactccaattagccataacactgttc" + | |
| "gtcaagatatagggggtcacccatgaatgtcctctaaccagaccatttcgttacacgaacgtatctgatgacttcttcgg" + | |
| "gaaattagttccctactcgtgtactccaattagccataacactgttcgtcaagatatagggggtcacccatgaatgtcct" + | |
| "ctaaccagaccatttcgttacacgaacgtatcttcggggcgtatgcgatgaaattagttccctactcgtgtactccaatt" + | |
| "agccataacactgttcgtcaagatatagggggtcacccatgaatgtcctctaaccagaccatttcgttacacgaacgtat" + | |
| "ctgatgacttcttcgggaaattagttccctactcgtgtactccaattagccataacactgttcgtcaagatatagggggt" + | |
| "cacccatgaatgtcctctaaccagaccatttcgttacacgaacgtatcttcggggcgtat" | |
| PATTERN = "ctccag" | |
| def reverse_strand(strand, out = '') | |
| reverse = strand.reverse | |
| # DNA opposites | |
| key = { | |
| a: 't', | |
| t: 'a', | |
| c: 'g', | |
| g: 'c' | |
| } | |
| reverse.length.times do |i| | |
| out += key[reverse[i].to_sym] | |
| end | |
| return out | |
| end | |
| def search_strand(strand, pattern) | |
| out = { | |
| pattern: pattern, | |
| matches: [] | |
| } | |
| strand.length.times do |i| | |
| new_pattern = strand[i...i+pattern.length] | |
| if new_pattern == pattern | |
| out[:matches] << {start: i, finish: i+pattern.length} | |
| end | |
| end | |
| return out | |
| end | |
| puts "Direct: #{search_strand(STRAND, PATTERN)}" | |
| puts "Reverse: #{search_strand(reverse_strand(STRAND), PATTERN)}" | |
| # => | |
| # Direct: {:pattern=>"ctccag", :matches=>[{:start=>28, :finish=>34}, {:start=>401, :finish=>407}]} | |
| # Reverse: {:pattern=>"ctccag", :matches=>[]} |
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