Bioinformatics/Global alignment: Difference between revisions
Added 11l
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=={{header|11l}}==
{{trans|Nim}}
<lang 11l>-V ACGT = [‘A’, ‘C’, ‘G’, ‘T’]
F permutations(slist)
V l = sorted(slist)
V r = [l]
L l.next_permutation()
r [+]= copy(l)
R r
F printCounts(dnaSeq)
DefaultDict[Char, Int] counts
L(c) dnaSeq
counts[c]++
print("\nNucleotide counts for #.:\n".format(dnaSeq))
L(base) :ACGT
print(‘#10 #11’.format(base, counts[base]))
V others = 0
L(base) counts.keys()
I base !C :ACGT
others += counts[base]
print(‘ Other #11’.format(others))
print(‘ --------------------’)
print(‘ Total length #7’.format(dnaSeq.len))
F headTailOverlap(s1, s2)
V start = 0
L
V? n = s1.find(s2[0], start)
I n == N
R 0
start = n
I s2.starts_with(s1[start..])
R s1.len - start
start++
F deduplicate(slist)
[String] r
V s = Set(slist)
L(s1) s
V i = L.index
L(s2) s
I L.index != i & s1 C s2
L.break
L.was_no_break
r.append(s1)
R r
F shortestCommonSuperstring(sl)
V slist = deduplicate(sl)
V result = slist.join(‘’)
L(perm) permutations(slist)
String sup = perm[0]
L(i) 0 .< slist.len - 1
V overlapPos = headTailOverlap(perm[i], perm[i + 1])
sup ‘’= perm[i + 1][overlapPos..]
I sup.len < result.len
result = sup
R result
V TestSequences = [
[‘TA’, ‘AAG’, ‘TA’, ‘GAA’, ‘TA’],
[‘CATTAGGG’, ‘ATTAG’, ‘GGG’, ‘TA’],
[‘AAGAUGGA’, ‘GGAGCGCAUC’, ‘AUCGCAAUAAGGA’],
[‘ATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTAT’,
‘GGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGT’,
‘CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA’,
‘TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC’,
‘AACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT’,
‘GCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTC’,
‘CGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCT’,
‘TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC’,
‘CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGC’,
‘GATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATT’,
‘TTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC’,
‘CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA’,
‘TCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGA’]]
L(test) TestSequences
V scs = shortestCommonSuperstring(test)
printCounts(scs)</lang>
{{out}}
<pre>
Nucleotide counts for GAAGTA:
A 3
C 0
G 2
T 1
Other 0
--------------------
Total length 6
Nucleotide counts for CATTAGGG:
A 2
C 1
G 3
T 2
Other 0
--------------------
Total length 8
Nucleotide counts for AAGAUGGAGCGCAUCGCAAUAAGGA:
A 10
C 4
G 8
T 0
Other 3
--------------------
Total length 25
Nucleotide counts for CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA:
A 74
C 57
G 75
T 94
Other 0
--------------------
Total length 300
</pre>
=={{header|Go}}==
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