Bioinformatics/Global alignment: Difference between revisions
m
→{{header|Phix}}
m (→{{header|Phix}}: "stable" not actually needed) |
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Line 192:
string ncf = "Nucleotide counts for :"
printf(1,"%s%s\n",{ncf,join(split_by(dna,50),"\n"&repeat(' ',length(ncf)))})
printf(1,"
end for
end procedure
function deduplicate(sequence ss)
-- Remove
sequence filtered = {}
for i=1 to length(ss) do
Line 216:
procedure shortest_common_superstring(sequence ss)
-- Returns shortest common superstring of a
ss = deduplicate(unique(ss))
sequence shortestsuper = {join(ss,"")}
Line 266:
papply(tests, shortest_common_superstring)</lang>
{{out}}
(Shows three length-6 results for the first test)
<pre>
Nucleotide counts for :TAAGAA
Base counts: Other:0, A:4, C:0, G:1, T:1, total:6
Nucleotide counts for :GAAGTA
Base counts: Other:0, A:3, C:0, G:2, T:1, total:6
Nucleotide counts for :TAGAAG
Base counts: Other:0, A:3, C:0, G:2, T:1, total:6
Nucleotide counts for :CATTAGGG
Base counts: Other:0, A:2, C:1, G:3, T:2, total:8
Nucleotide counts for :AAGAUGGAGCGCAUCGCAAUAAGGA
Base counts: Other:3, A:10, C:4, G:8, T:0, total:25
Line 293 ⟶ 289:
CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
Base counts: Other:0, A:74, C:57, G:75, T:94, total:300
</pre>
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