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Bioinformatics/Global alignment: Difference between revisions

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Bioinformatics/Global alignment (view source)

Revision as of 21:19, 18 May 2021

789 bytes added ,  2 years ago
m
→‎{{header|Phix}}: fixed a couple of syntax glitches, added personal tag
m (→‎{{header|Phix}}: fixed a couple of syntax glitches, added personal tag)
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=={{header|Phix}}==
<!--<lang Phix>(phixonline)-->
<span style="color: #008080;">procedure</span> <span style="color: #000000;">printcounts</span><span style="color: #0000FF;">(</span><span style="color: #004080;">sequence</span> <span style="color: #000000;">ss</span><span style="color: #0000FF;">)</span>
<span style="color: #000080;font-style:italic;">-- Given DNA sequence(s), report the sequence, length and base counts</span>
<span style="color: #008080;">for</span> <span style="color: #000000;">i</span><span style="color: #0000FF;">=</span><span style="color: #000000;">1</span> <span style="color: #008080;">to</span> <span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">ss</span><span style="color: #0000FF;">)</span> <span style="color: #008080;">do</span>
<span style="color: #004080;">string</span> <span style="color: #000000;">dna</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">ss</span><span style="color: #0000FF;">[</span><span style="color: #000000;">i</span><span style="color: #0000FF;">]</span>
<span style="color: #004080;">sequence</span> <span style="color: #000000;">acgt</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">repeat</span><span style="color: #0000FF;">(</span><span style="color: #000000;">0</span><span style="color: #0000FF;">,</span><span style="color: #000000;">6</span><span style="color: #0000FF;">)</span>
<span style="color: #008080;">for</span> <span style="color: #000000;">j</span><span style="color: #0000FF;">=</span><span style="color: #000000;">1</span> <span style="color: #008080;">to</span> <span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">dna</span><span style="color: #0000FF;">)</span> <span style="color: #008080;">do</span>
<span style="color: #000000;">acgt</span><span style="color: #0000FF;">[</span><span style="color: #7060A8;">find</span><span style="color: #0000FF;">(</span><span style="color: #000000;">dna</span><span style="color: #0000FF;">[</span><span style="color: #000000;">j</span style="color: #0000FF;">]<span style="color: #0000FF;">],</span><span style="color: #008000;">"ACGT"</span style="color: #0000FF;">)<span style="color: #0000FF;">)+</span><span style="color: #000000;">1</span><span style="color: #0000FF;">]</span> <span style="color: #0000FF;">+=</span> <span style="color: #000000;">1</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">for</span>
<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><span style="color: #0000FF;">(</span><span style="color: #000000;">acgt</span><span style="color: #0000FF;">)</span>
<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>
<span style="color: #7060A8;">printf</span><span style="color: #0000FF;">(</span><span style="color: #000000;">1</span><span style="color: #0000FF;">,</span><span style="color: #008000;">"%s%s\n"</span style="color: #0000FF;">,<span style="color: #0000FF;">,{</span><span style="color: #000000;">ncf</span><span style="color: #0000FF;">,</span><span style="color: #7060A8;">join</span><span style="color: #0000FF;">(</span><span style="color: #7060A8;">split_by</span><span style="color: #0000FF;">(</span><span style="color: #000000;">dna</span><span style="color: #0000FF;">,</span><span style="color: #000000;">50</span><span style="color: #0000FF;">),</span style="color: #0000FF;">,<span style="color: #008000;">"\n"</span><span style="color: #0000FF;">&</span><span style="color: #7060A8;">repeat</span><span style="color: #0000FF;">(</span><span style="color: #008000;">' '</span><span style="color: #0000FF;">,</span style="color: #7060A8;">length<span style="color: #0000FF7060A8;">(length</span style="color: #000000;">ncf<span style="color: #0000FF;">)(</span style="color: #0000FF;">)<span style="color: #0000FF000000;">)ncf</span style="color: #0000FF;">}<span style="color: #0000FF;">)))})</span>
<span style="color: #7060A8;">printf</span><span style="color: #0000FF;">(</span><span style="color: #000000;">1</span><span style="color: #0000FF;">,</span><span style="color: #008000;">"Base counts: Other:%d, A:%d, C:%d, G:%d, T:%d, total:%d\n\n"</span><span style="color: #0000FF;">,</span><span style="color: #000000;">acgt</span><span style="color: #0000FF;">)</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">for</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">procedure</span>
<span style="color: #008080;">function</span> <span style="color: #000000;">deduplicate</span><span style="color: #0000FF;">(</span><span style="color: #004080;">sequence</span> <span style="color: #000000;">ss</span><span style="color: #0000FF;">)</span>
<span style="color: #000080;font-style:italic;">-- Remove any strings contained within a larger string from a set of strings</span>
<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>
<span style="color: #008080;">for</span> <span style="color: #000000;">i</span><span style="color: #0000FF;">=</span><span style="color: #000000;">1</span> <span style="color: #008080;">to</span> <span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">ss</span><span style="color: #0000FF;">)</span> <span style="color: #008080;">do</span>
<span style="color: #004080;">string</span> <span style="color: #000000;">si</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">ss</span><span style="color: #0000FF;">[</span><span style="color: #000000;">i</span><span style="color: #0000FF;">]</span>
<span style="color: #004080;">bool</span> <span style="color: #000000;">found</span> <span style="color: #0000FF;">=</span> <span style="color: #004600;">false</span>
<span style="color: #008080;">for</span> <span style="color: #000000;">j</span><span style="color: #0000FF;">=</span><span style="color: #000000;">1</span> <span style="color: #008080;">to</span> <span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">ss</span><span style="color: #0000FF;">)</span> <span style="color: #008080;">do</span>
<span style="color: #008080;">if</span> <span style="color: #000000;">i</span><span style="color: #0000FF;">!=</span><span style="color: #000000;">j</span> <span style="color: #008080;">and</span> <span style="color: #7060A8;">match</span><span style="color: #0000FF;">(</span><span style="color: #000000;">si</span><span style="color: #0000FF;">,</span><span style="color: #000000;">ss</span><span style="color: #0000FF;">[</span><span style="color: #000000;">j</span style="color: #0000FF;">]<span style="color: #0000FF;">])</span> <span style="color: #008080;">then</span>
<span style="color: #000000;">found</span> <span style="color: #0000FF;">=</span> <span style="color: #004600;">true</span>
<span style="color: #008080;">exit</span>
Line 654:
<span style="color: #008080;">end</span> <span style="color: #008080;">for</span>
<span style="color: #008080;">if</span> <span style="color: #008080;">not</span> <span style="color: #000000;">found</span> <span style="color: #008080;">then</span>
<span style="color: #000000;">filtered</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">append</span><span style="color: #0000FF;">(</span><span style="color: #000000;">filtered</span><span style="color: #0000FF;">,</span> <span style="color: #000000;">si</span><span style="color: #0000FF;">)</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">if</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">for</span>
Line 660:
<span style="color: #008080;">end</span> <span style="color: #008080;">function</span>
<span style="color: #008080;">procedure</span> <span style="color: #000000;">shortest_common_superstring</span><span style="color: #0000FF;">(</span><span style="color: #004080;">sequence</span> <span style="color: #000000;">ss</span><span style="color: #0000FF;">)</span>
<span style="color: #000080;font-style:italic;">-- Returns shortest common superstring of a set of strings</span>
<span style="color: #000000;">ss</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">deduplicate</span><span style="color: #0000FF;">(</span><span style="color: #7060A8;">unique</span><span style="color: #0000FF;">(</span><span style="color: #000000;">ss</span style="color: #0000FF;">)<span style="color: #0000FF;">))</span>
<span style="color: #004080;">sequence</span> <span style="color: #000000;">shortestsuper</span> <span style="color: #0000FF;">=</span> <span style="color: #0000FF;">{</span><span style="color: #7060A8;">join</span><span style="color: #0000FF;">(</span><span style="color: #000000;">ss</span><span style="color: #0000FF;">,</span><span style="color: #008000;">""</span style="color: #0000FF;">)<span style="color: #0000FF;">)}</span>
<span style="color: #004080;">integer</span> <span style="color: #000000;">shortest</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">shortestsuper</span><span style="color: #0000FF;">[</span><span style="color: #000000;">1</span style="color: #0000FF;">]<span style="color: #0000FF;">])</span>
<span style="color: #008080;">for</span> <span style="color: #000000;">p</span><span style="color: #0000FF;">=</span><span style="color: #000000;">1</span> <span style="color: #008080;">to</span> <span style="color: #0000007060A8;">factorial</span><span style="color: #0000FF;">(</span><span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">ss</span style="color: #0000FF;">)<span style="color: #0000FF;">))</span> <span style="color: #008080;">do</span>
<span style="color: #004080;">sequence</span> <span style="color: #000000;">perm</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">permute</span><span style="color: #0000FF;">(</span><span style="color: #000000;">p</span><span style="color: #0000FF;">,</span><span style="color: #000000;">ss</span><span style="color: #0000FF;">)</span>
<span style="color: #004080;">string</span> <span style="color: #000000;">sup</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">perm</span><span style="color: #0000FF;">[</span><span style="color: #000000;">1</span><span style="color: #0000FF;">]</span>
<span style="color: #008080;">for</span> <span style="color: #000000;">i</span><span style="color: #0000FF;">=</span><span style="color: #000000;">2</span> <span style="color: #008080;">to</span> <span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">perm</span><span style="color: #0000FF;">)</span> <span style="color: #008080;">do</span>
<span style="color: #004080;">string</span> <span style="color: #000000;">pi</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">perm</span><span style="color: #0000FF;">[</span><span style="color: #000000;">i</span><span style="color: #0000FF;">]</span>
<span style="color: #008080;">for</span> <span style="color: #000000;">j</span><span style="color: #0000FF;">=-</span style="color: #0000FF;">-<span style="color: #7060A8;">min</span><span style="color: #0000FF;">(</span><span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">pi</span style="color: #0000FF;">)<span style="color: #0000FF;">),</span><span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><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>
<span style="color: #004080;">string</span> <span style="color: #000000;">overlap</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">sup</span><span style="color: #0000FF;">[</span><span style="color: #000000;">j</span style="color: #0000FF;">..<span style="color: #0000FF;">..$<span style="color: #0000FF;">]</span>
<span style="color: #008080;">if</span> <span style="color: #000000;">overlap</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">pi</span><span style="color: #0000FF;">[</span><span style="color: #000000;">1</span><span style="color: #0000FF;">..</span><span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">overlap</span style="color: #0000FF;">)<span style="color: #0000FF;">)]</span> <span style="color: #008080;">then</span>
<span style="color: #000000;">sup</span> <span style="color: #0000FF;">&=</span> <span style="color: #000000;">pi</span><span style="color: #0000FF;">[</span><span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">overlap</span style="color: #0000FF;">)<span style="color: #0000FF;">)+</span><span style="color: #000000;">1</span style="color: #0000FF;">..<span style="color: #0000FF;">..$<span style="color: #0000FF;">]</span>
<span style="color: #000000;">pi</span> <span style="color: #0000FF;">=</span> <span style="color: #008000;">""</span>
<span style="color: #008080;">exit</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">if</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">for</span>
<span style="color: #008080;">if</span> <span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">pi</span><span style="color: #0000FF;">)</span> <span style="color: #008080;">then</span> <span style="color: #0000FF;">?</span><span style="color: #000000;">9</span><span style="color: #0000FF;">/</span><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>
<span style="color: #008080;">end</span> <span style="color: #008080;">for</span>
<span style="color: #008080;">if</span> <span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">sup</span><span style="color: #0000FF;">)</span> <span style="color: #0000FF;"><</span> <span style="color: #000000;">shortest</span> <span style="color: #008080;">then</span>
<span style="color: #000000;">shortest</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">sup</span><span style="color: #0000FF;">)</span>
<span style="color: #000000;">shortestsuper</span> <span style="color: #0000FF;">=</span> <span style="color: #0000FF;">{</span><span style="color: #000000;">sup</span><span style="color: #0000FF;">}</span>
<span style="color: #008080;">elsif</span> <span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">sup</span><span style="color: #0000FF;">)</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">shortest</span>
<span style="color: #008080;">and</span> <span style="color: #008080;">not</span> <span style="color: #7060A8;">find</span><span style="color: #0000FF;">(</span><span style="color: #000000;">sup</span><span style="color: #0000FF;">,</span><span style="color: #000000;">shortestsuper</span><span style="color: #0000FF;">)</span> <span style="color: #008080;">then</span>
<span style="color: #000000;">shortestsuper</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">append</span><span style="color: #0000FF;">(</span><span style="color: #000000;">shortestsuper</span><span style="color: #0000FF;">,</span><span style="color: #000000;">sup</span><span style="color: #0000FF;">)</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">if</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">for</span>
<span style="color: #000000;">printcounts</span><span style="color: #0000FF;">(</span><span style="color: #000000;">shortestsuper</span><span style="color: #0000FF;">)</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">procedure</span>
<span style="color: #008080;">constant</span> <span style="color: #000000;">tests</span> <span style="color: #0000FF;">=</span> <span style="color: #0000FF;">{</span>
<span style="color: #0000FF;">{</span><span style="color: #008000;">"TA"</span><span style="color: #0000FF;">,</span> <span style="color: #008000;">"AAG"</span><span style="color: #0000FF;">,</span> <span style="color: #008000;">"TA"</span><span style="color: #0000FF;">,</span> <span style="color: #008000;">"GAA"</span><span style="color: #0000FF;">,</span> <span style="color: #008000;">"TA"</span style="color: #0000FF;">}<span style="color: #0000FF;">},</span>
<span style="color: #0000FF;">{</span><span style="color: #008000;">"CATTAGGG"</span><span style="color: #0000FF;">,</span> <span style="color: #008000;">"ATTAG"</span><span style="color: #0000FF;">,</span> <span style="color: #008000;">"GGG"</span><span style="color: #0000FF;">,</span> <span style="color: #008000;">"TA"</span style="color: #0000FF;">}<span style="color: #0000FF;">},</span>
<span style="color: #0000FF;">{</span><span style="color: #008000;">"AAGAUGGA"</span><span style="color: #0000FF;">,</span> <span style="color: #008000;">"GGAGCGCAUC"</span><span style="color: #0000FF;">,</span> <span style="color: #008000;">"AUCGCAAUAAGGA"</span style="color: #0000FF;">}<span style="color: #0000FF;">},</span>
<span style="color: #0000FF;">{</span><span style="color: #008000;">"ATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTAT"</span><span style="color: #0000FF;">,</span>
<span style="color: #008000;">"GGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGT"</span><span style="color: #0000FF;">,</span>
<span style="color: #008000;">"CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA"</span><span style="color: #0000FF;">,</span>
<span style="color: #008000;">"TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC"</span><span style="color: #0000FF;">,</span>
<span style="color: #008000;">"AACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT"</span><span style="color: #0000FF;">,</span>
<span style="color: #008000;">"GCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTC"</span><span style="color: #0000FF;">,</span>
<span style="color: #008000;">"CGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCT"</span><span style="color: #0000FF;">,</span>
<span style="color: #008000;">"TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC"</span><span style="color: #0000FF;">,</span>
<span style="color: #008000;">"CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGC"</span><span style="color: #0000FF;">,</span>
<span style="color: #008000;">"GATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATT"</span><span style="color: #0000FF;">,</span>
<span style="color: #008000;">"TTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC"</span><span style="color: #0000FF;">,</span>
<span style="color: #008000;">"CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA"</span><span style="color: #0000FF;">,</span>
<span style="color: #008000;">"TCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGA"</span><span style="color: #0000FF;">}</span>
<span style="color: #0000FF;">}</span>
<span style="color: #7060A8;">papply</span><span style="color: #0000FF;">(</span><span style="color: #000000;">tests</span><span style="color: #0000FF;">,</span> <span style="color: #000000;">shortest_common_superstring</span><span style="color: #0000FF;">)</span>
<!--</lang>-->
{{out}}
Petelomax
7,794

edits

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