Bioinformatics/Global alignment: Difference between revisions
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=={{header|Phix}}== |
=={{header|Phix}}== |
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<lang Phix> |
<!--<lang Phix>--> |
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<span style="color: #008080;">procedure</span> <span style="color: #000000;">printcounts<span style="color: #0000FF;">(<span style="color: #004080;">sequence</span> <span style="color: #000000;">ss<span style="color: #0000FF;">)</span> |
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-- Given DNA sequence(s), report the sequence, length and base counts |
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<span style="color: #000080;font-style:italic;">-- Given DNA sequence(s), report the sequence, length and base counts</span> |
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for i=1 to length(ss) do |
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<span style="color: #008080;">for</span> <span style="color: #000000;">i<span style="color: #0000FF;">=<span style="color: #000000;">1</span> <span style="color: #008080;">to</span> <span style="color: #7060A8;">length<span style="color: #0000FF;">(<span style="color: #000000;">ss<span style="color: #0000FF;">)</span> <span style="color: #008080;">do</span> |
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string dna = ss[i] |
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<span style="color: #004080;">string</span> <span style="color: #000000;">dna</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">ss<span style="color: #0000FF;">[<span style="color: #000000;">i<span style="color: #0000FF;">]</span> |
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sequence acgt = repeat(0,6) |
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<span style="color: #004080;">sequence</span> <span style="color: #000000;">acgt</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">repeat<span style="color: #0000FF;">(<span style="color: #000000;">0<span style="color: #0000FF;">,<span style="color: #000000;">6<span style="color: #0000FF;">)</span> |
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for j=1 to length(dna) do |
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<span style="color: #008080;">for</span> <span style="color: #000000;">j<span style="color: #0000FF;">=<span style="color: #000000;">1</span> <span style="color: #008080;">to</span> <span style="color: #7060A8;">length<span style="color: #0000FF;">(<span style="color: #000000;">dna<span style="color: #0000FF;">)</span> <span style="color: #008080;">do</span> |
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acgt[find(dna[j],"ACGT")+1] += 1 |
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<span style="color: #000000;">acgt<span style="color: #0000FF;">[<span style="color: #7060A8;">find<span style="color: #0000FF;">(<span style="color: #000000;">dna<span style="color: #0000FF;">[<span style="color: #000000;">j<span style="color: #0000FF;">]<span style="color: #0000FF;">,<span style="color: #008000;">"ACGT"<span style="color: #0000FF;">)<span style="color: #0000FF;">+<span style="color: #000000;">1<span style="color: #0000FF;">]</span> <span style="color: #0000FF;">+=</span> <span style="color: #000000;">1</span> |
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end for |
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<span style="color: #008080;">end</span> <span style="color: #008080;">for</span> |
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acgt[$] = sum(acgt) |
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<span style="color: #000000;">acgt<span style="color: #0000FF;">[<span style="color: #0000FF;">$<span style="color: #0000FF;">]</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">sum<span style="color: #0000FF;">(<span style="color: #000000;">acgt<span style="color: #0000FF;">)</span> |
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string ncf = "Nucleotide counts for :" |
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<span style="color: #004080;">string</span> <span style="color: #000000;">ncf</span> <span style="color: #0000FF;">=</span> <span style="color: #008000;">"Nucleotide counts for :"</span> |
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printf(1,"%s%s\n",{ncf,join(split_by(dna,50),"\n"&repeat(' ',length(ncf)))}) |
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<span style="color: #7060A8;">printf<span style="color: #0000FF;">(<span style="color: #000000;">1<span style="color: #0000FF;">,<span style="color: #008000;">"%s%s\n"<span style="color: #0000FF;">,<span style="color: #0000FF;">{<span style="color: #000000;">ncf<span style="color: #0000FF;">,<span style="color: #7060A8;">join<span style="color: #0000FF;">(<span style="color: #7060A8;">split_by<span style="color: #0000FF;">(<span style="color: #000000;">dna<span style="color: #0000FF;">,<span style="color: #000000;">50<span style="color: #0000FF;">)<span style="color: #0000FF;">,<span style="color: #008000;">"\n"<span style="color: #0000FF;">&<span style="color: #7060A8;">repeat<span style="color: #0000FF;">(<span style="color: #008000;">' '<span style="color: #0000FF;">,<span style="color: #7060A8;">length<span style="color: #0000FF;">(<span style="color: #000000;">ncf<span style="color: #0000FF;">)<span style="color: #0000FF;">)<span style="color: #0000FF;">)<span style="color: #0000FF;">}<span style="color: #0000FF;">)</span> |
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printf(1,"Base counts: Other:%d, A:%d, C:%d, G:%d, T:%d, total:%d\n\n",acgt) |
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<span style="color: #7060A8;">printf<span style="color: #0000FF;">(<span style="color: #000000;">1<span style="color: #0000FF;">,<span style="color: #008000;">"Base counts: Other:%d, A:%d, C:%d, G:%d, T:%d, total:%d\n\n"<span style="color: #0000FF;">,<span style="color: #000000;">acgt<span style="color: #0000FF;">)</span> |
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end for |
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<span style="color: #008080;">end</span> <span style="color: #008080;">for</span> |
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end procedure |
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<span style="color: #008080;">end</span> <span style="color: #008080;">procedure</span> |
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function deduplicate(sequence ss) |
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<span style="color: #008080;">function</span> <span style="color: #000000;">deduplicate<span style="color: #0000FF;">(<span style="color: #004080;">sequence</span> <span style="color: #000000;">ss<span style="color: #0000FF;">)</span> |
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-- Remove any strings contained within a larger string from a set of strings |
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<span style="color: #000080;font-style:italic;">-- Remove any strings contained within a larger string from a set of strings</span> |
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sequence filtered = {} |
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<span style="color: #004080;">sequence</span> <span style="color: #000000;">filtered</span> <span style="color: #0000FF;">=</span> <span style="color: #0000FF;">{<span style="color: #0000FF;">}</span> |
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for i=1 to length(ss) do |
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<span style="color: #008080;">for</span> <span style="color: #000000;">i<span style="color: #0000FF;">=<span style="color: #000000;">1</span> <span style="color: #008080;">to</span> <span style="color: #7060A8;">length<span style="color: #0000FF;">(<span style="color: #000000;">ss<span style="color: #0000FF;">)</span> <span style="color: #008080;">do</span> |
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string si = ss[i] |
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<span style="color: #004080;">string</span> <span style="color: #000000;">si</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">ss<span style="color: #0000FF;">[<span style="color: #000000;">i<span style="color: #0000FF;">]</span> |
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bool found = false |
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<span style="color: #004080;">bool</span> <span style="color: #000000;">found</span> <span style="color: #0000FF;">=</span> <span style="color: #004600;">false</span> |
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for j=1 to length(ss) do |
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<span style="color: #008080;">for</span> <span style="color: #000000;">j<span style="color: #0000FF;">=<span style="color: #000000;">1</span> <span style="color: #008080;">to</span> <span style="color: #7060A8;">length<span style="color: #0000FF;">(<span style="color: #000000;">ss<span style="color: #0000FF;">)</span> <span style="color: #008080;">do</span> |
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if i!=j and match(si,ss[j]) then |
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<span style="color: #008080;">if</span> <span style="color: #000000;">i<span style="color: #0000FF;">!=<span style="color: #000000;">j</span> <span style="color: #008080;">and</span> <span style="color: #7060A8;">match<span style="color: #0000FF;">(<span style="color: #000000;">si<span style="color: #0000FF;">,<span style="color: #000000;">ss<span style="color: #0000FF;">[<span style="color: #000000;">j<span style="color: #0000FF;">]<span style="color: #0000FF;">)</span> <span style="color: #008080;">then</span> |
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found = true |
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<span style="color: #000000;">found</span> <span style="color: #0000FF;">=</span> <span style="color: #004600;">true</span> |
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exit |
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<span style="color: #008080;">exit</span> |
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<span style="color: #008080;">end</span> <span style="color: #008080;">if</span> |
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end for |
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<span style="color: #008080;">end</span> <span style="color: #008080;">for</span> |
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if not found then |
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<span style="color: #008080;">if</span> <span style="color: #008080;">not</span> <span style="color: #000000;">found</span> <span style="color: #008080;">then</span> |
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filtered = append(filtered, si) |
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<span style="color: #000000;">filtered</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">append<span style="color: #0000FF;">(<span style="color: #000000;">filtered<span style="color: #0000FF;">,</span> <span style="color: #000000;">si<span style="color: #0000FF;">)</span> |
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end if |
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<span style="color: #008080;">end</span> <span style="color: #008080;">if</span> |
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end for |
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<span style="color: #008080;">end</span> <span style="color: #008080;">for</span> |
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return filtered |
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<span style="color: #008080;">return</span> <span style="color: #000000;">filtered</span> |
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end function |
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<span style="color: #008080;">end</span> <span style="color: #008080;">function</span> |
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procedure shortest_common_superstring(sequence ss) |
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<span style="color: #008080;">procedure</span> <span style="color: #000000;">shortest_common_superstring<span style="color: #0000FF;">(<span style="color: #004080;">sequence</span> <span style="color: #000000;">ss<span style="color: #0000FF;">)</span> |
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-- Returns shortest common superstring of a set of strings |
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<span style="color: #000080;font-style:italic;">-- Returns shortest common superstring of a set of strings</span> |
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ss = deduplicate(unique(ss)) |
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<span style="color: #000000;">ss</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">deduplicate<span style="color: #0000FF;">(<span style="color: #7060A8;">unique<span style="color: #0000FF;">(<span style="color: #000000;">ss<span style="color: #0000FF;">)<span style="color: #0000FF;">)</span> |
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sequence shortestsuper = {join(ss,"")} |
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<span style="color: #004080;">sequence</span> <span style="color: #000000;">shortestsuper</span> <span style="color: #0000FF;">=</span> <span style="color: #0000FF;">{<span style="color: #7060A8;">join<span style="color: #0000FF;">(<span style="color: #000000;">ss<span style="color: #0000FF;">,<span style="color: #008000;">""<span style="color: #0000FF;">)<span style="color: #0000FF;">}</span> |
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integer shortest = length(shortestsuper[1]) |
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<span style="color: #004080;">integer</span> <span style="color: #000000;">shortest</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">length<span style="color: #0000FF;">(<span style="color: #000000;">shortestsuper<span style="color: #0000FF;">[<span style="color: #000000;">1<span style="color: #0000FF;">]<span style="color: #0000FF;">)</span> |
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for p=1 to factorial(length(ss)) do |
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<span style="color: #008080;">for</span> <span style="color: #000000;">p<span style="color: #0000FF;">=<span style="color: #000000;">1</span> <span style="color: #008080;">to</span> <span style="color: #000000;">factorial<span style="color: #0000FF;">(<span style="color: #7060A8;">length<span style="color: #0000FF;">(<span style="color: #000000;">ss<span style="color: #0000FF;">)<span style="color: #0000FF;">)</span> <span style="color: #008080;">do</span> |
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sequence perm = permute(p,ss) |
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<span style="color: #004080;">sequence</span> <span style="color: #000000;">perm</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">permute<span style="color: #0000FF;">(<span style="color: #000000;">p<span style="color: #0000FF;">,<span style="color: #000000;">ss<span style="color: #0000FF;">)</span> |
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string sup = perm[1] |
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<span style="color: #004080;">string</span> <span style="color: #000000;">sup</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">perm<span style="color: #0000FF;">[<span style="color: #000000;">1<span style="color: #0000FF;">]</span> |
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for i=2 to length(perm) do |
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<span style="color: #008080;">for</span> <span style="color: #000000;">i<span style="color: #0000FF;">=<span style="color: #000000;">2</span> <span style="color: #008080;">to</span> <span style="color: #7060A8;">length<span style="color: #0000FF;">(<span style="color: #000000;">perm<span style="color: #0000FF;">)</span> <span style="color: #008080;">do</span> |
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string pi = perm[i] |
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<span style="color: #004080;">string</span> <span style="color: #000000;">pi</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">perm<span style="color: #0000FF;">[<span style="color: #000000;">i<span style="color: #0000FF;">]</span> |
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for j=-min(length(pi),length(sup)) to 0 do |
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<span style="color: #008080;">for</span> <span style="color: #000000;">j<span style="color: #0000FF;">=<span style="color: #0000FF;">-<span style="color: #7060A8;">min<span style="color: #0000FF;">(<span style="color: #7060A8;">length<span style="color: #0000FF;">(<span style="color: #000000;">pi<span style="color: #0000FF;">)<span style="color: #0000FF;">,<span style="color: #7060A8;">length<span style="color: #0000FF;">(<span style="color: #000000;">sup<span style="color: #0000FF;">)<span style="color: #0000FF;">)</span> <span style="color: #008080;">to</span> <span style="color: #000000;">0</span> <span style="color: #008080;">do</span> |
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string overlap = sup[j..$] |
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<span style="color: #004080;">string</span> <span style="color: #000000;">overlap</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">sup<span style="color: #0000FF;">[<span style="color: #000000;">j<span style="color: #0000FF;">..<span style="color: #0000FF;">$<span style="color: #0000FF;">]</span> |
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if overlap = pi[1..length(overlap)] then |
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<span style="color: #008080;">if</span> <span style="color: #000000;">overlap</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">pi<span style="color: #0000FF;">[<span style="color: #000000;">1<span style="color: #0000FF;">..<span style="color: #7060A8;">length<span style="color: #0000FF;">(<span style="color: #000000;">overlap<span style="color: #0000FF;">)<span style="color: #0000FF;">]</span> <span style="color: #008080;">then</span> |
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sup &= pi[length(overlap)+1..$] |
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<span style="color: #000000;">sup</span> <span style="color: #0000FF;">&=</span> <span style="color: #000000;">pi<span style="color: #0000FF;">[<span style="color: #7060A8;">length<span style="color: #0000FF;">(<span style="color: #000000;">overlap<span style="color: #0000FF;">)<span style="color: #0000FF;">+<span style="color: #000000;">1<span style="color: #0000FF;">..<span style="color: #0000FF;">$<span style="color: #0000FF;">]</span> |
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pi = "" |
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<span style="color: #000000;">pi</span> <span style="color: #0000FF;">=</span> <span style="color: #008000;">""</span> |
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exit |
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<span style="color: #008080;">exit</span> |
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<span style="color: #008080;">end</span> <span style="color: #008080;">if</span> |
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end for |
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<span style="color: #008080;">end</span> <span style="color: #008080;">for</span> |
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if length(pi) then ?9/0 end if -- (sanity chk) |
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<span style="color: #008080;">if</span> <span style="color: #7060A8;">length<span style="color: #0000FF;">(<span style="color: #000000;">pi<span style="color: #0000FF;">)</span> <span style="color: #008080;">then</span> <span style="color: #0000FF;">?<span style="color: #000000;">9<span style="color: #0000FF;">/<span style="color: #000000;">0</span> <span style="color: #008080;">end</span> <span style="color: #008080;">if</span> <span style="color: #000080;font-style:italic;">-- (sanity chk)</span> |
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end for |
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<span style="color: #008080;">end</span> <span style="color: #008080;">for</span> |
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if length(sup) < shortest then |
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<span style="color: #008080;">if</span> <span style="color: #7060A8;">length<span style="color: #0000FF;">(<span style="color: #000000;">sup<span style="color: #0000FF;">)</span> <span style="color: #0000FF;"><</span> <span style="color: #000000;">shortest</span> <span style="color: #008080;">then</span> |
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shortest = length(sup) |
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<span style="color: #000000;">shortest</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">length<span style="color: #0000FF;">(<span style="color: #000000;">sup<span style="color: #0000FF;">)</span> |
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shortestsuper = {sup} |
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<span style="color: #000000;">shortestsuper</span> <span style="color: #0000FF;">=</span> <span style="color: #0000FF;">{<span style="color: #000000;">sup<span style="color: #0000FF;">}</span> |
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elsif length(sup) = shortest |
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<span style="color: #008080;">elsif</span> <span style="color: #7060A8;">length<span style="color: #0000FF;">(<span style="color: #000000;">sup<span style="color: #0000FF;">)</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">shortest</span> |
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and not find(sup,shortestsuper) then |
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<span style="color: #008080;">and</span> <span style="color: #008080;">not</span> <span style="color: #7060A8;">find<span style="color: #0000FF;">(<span style="color: #000000;">sup<span style="color: #0000FF;">,<span style="color: #000000;">shortestsuper<span style="color: #0000FF;">)</span> <span style="color: #008080;">then</span> |
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shortestsuper = append(shortestsuper,sup) |
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<span style="color: #000000;">shortestsuper</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">append<span style="color: #0000FF;">(<span style="color: #000000;">shortestsuper<span style="color: #0000FF;">,<span style="color: #000000;">sup<span style="color: #0000FF;">)</span> |
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end if |
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<span style="color: #008080;">end</span> <span style="color: #008080;">if</span> |
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end for |
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<span style="color: #008080;">end</span> <span style="color: #008080;">for</span> |
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printcounts(shortestsuper) |
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<span style="color: #000000;">printcounts<span style="color: #0000FF;">(<span style="color: #000000;">shortestsuper<span style="color: #0000FF;">)</span> |
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end procedure |
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<span style="color: #008080;">end</span> <span style="color: #008080;">procedure</span> |
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constant tests = { |
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<span style="color: #008080;">constant</span> <span style="color: #000000;">tests</span> <span style="color: #0000FF;">=</span> <span style="color: #0000FF;">{</span> |
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{"TA", "AAG", "TA", "GAA", "TA"}, |
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<span style="color: #0000FF;">{<span style="color: #008000;">"TA"<span style="color: #0000FF;">,</span> <span style="color: #008000;">"AAG"<span style="color: #0000FF;">,</span> <span style="color: #008000;">"TA"<span style="color: #0000FF;">,</span> <span style="color: #008000;">"GAA"<span style="color: #0000FF;">,</span> <span style="color: #008000;">"TA"<span style="color: #0000FF;">}<span style="color: #0000FF;">,</span> |
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{"CATTAGGG", "ATTAG", "GGG", "TA"}, |
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<span style="color: #0000FF;">{<span style="color: #008000;">"CATTAGGG"<span style="color: #0000FF;">,</span> <span style="color: #008000;">"ATTAG"<span style="color: #0000FF;">,</span> <span style="color: #008000;">"GGG"<span style="color: #0000FF;">,</span> <span style="color: #008000;">"TA"<span style="color: #0000FF;">}<span style="color: #0000FF;">,</span> |
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{"AAGAUGGA", "GGAGCGCAUC", "AUCGCAAUAAGGA"}, |
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<span style="color: #0000FF;">{<span style="color: #008000;">"AAGAUGGA"<span style="color: #0000FF;">,</span> <span style="color: #008000;">"GGAGCGCAUC"<span style="color: #0000FF;">,</span> <span style="color: #008000;">"AUCGCAAUAAGGA"<span style="color: #0000FF;">}<span style="color: #0000FF;">,</span> |
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{"ATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTAT", |
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<span style="color: #0000FF;">{<span style="color: #008000;">"ATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTAT"<span style="color: #0000FF;">,</span> |
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"GGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGT", |
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<span style="color: #008000;">"GGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGT"<span style="color: #0000FF;">,</span> |
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"CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA", |
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<span style="color: #008000;">"CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA"<span style="color: #0000FF;">,</span> |
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"TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC", |
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<span style="color: #008000;">"TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC"<span style="color: #0000FF;">,</span> |
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"AACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT", |
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<span style="color: #008000;">"AACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT"<span style="color: #0000FF;">,</span> |
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"GCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTC", |
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<span style="color: #008000;">"GCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTC"<span style="color: #0000FF;">,</span> |
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"CGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCT", |
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<span style="color: #008000;">"CGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCT"<span style="color: #0000FF;">,</span> |
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"TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC", |
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<span style="color: #008000;">"TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC"<span style="color: #0000FF;">,</span> |
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"CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGC", |
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<span style="color: #008000;">"CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGC"<span style="color: #0000FF;">,</span> |
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"GATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATT", |
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<span style="color: #008000;">"GATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATT"<span style="color: #0000FF;">,</span> |
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"TTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC", |
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<span style="color: #008000;">"TTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC"<span style="color: #0000FF;">,</span> |
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"CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA", |
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<span style="color: #008000;">"CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA"<span style="color: #0000FF;">,</span> |
|||
"TCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGA"} |
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<span style="color: #008000;">"TCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGA"<span style="color: #0000FF;">}</span> |
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} |
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<span style="color: #0000FF;">}</span> |
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papply(tests, shortest_common_superstring)</lang> |
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<span style="color: #7060A8;">papply<span style="color: #0000FF;">(<span style="color: #000000;">tests<span style="color: #0000FF;">,</span> <span style="color: #000000;">shortest_common_superstring<span style="color: #0000FF;">) |
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<!--</lang>--> |
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{{out}} |
{{out}} |
||
(Shows three length-6 results for the first test) |
(Shows three length-6 results for the first test) |