Bioinformatics/Global alignment: Difference between revisions

{{trans|Nim}}

 

 

F permutations(slist)

L(test) TestSequences

V scs = shortestCommonSuperstring(test)

 

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=={{header|Go}}==

{{trans|Julia}}

 

import (

printCounts(scs)

}

 

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{{works with|jq}}

'''Works with gojq, the Go implementation of jq'''

### Generic helper functions

 

range(0;length) as $i

| [.[$i]] + (del(.[$i])|permutations)

# Give a synoptic view of the input string,

# highlighting the occurrence of ACGTU letters

else . end)

| .shortestsuper;

'''The specific tasks'''

def examples:

[

| "Task \($i+1):", ($examples[$i]|t), "";

 

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<pre>

 

=={{header|Julia}}==

 

""" Given a DNA sequence, report the sequence, length and base counts"""

printcounts(scs)

end

<pre>

Nucleotide counts for TAAGAA:

=={{header|Nim}}==

{{trans|Wren}}

 

const ACGT = ['A', 'C', 'G', 'T'] # Four DNA bases.

for test in TestSequences:

let scs = test.shortestCommonSuperstring

 

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Here nearly no runtime.But see [[N-queens_problem]] that using permutation is not the way for > 17<BR>

Of course this is more a traveling salesman problem.

program BaseInDNA;

{$IFDEF FPC}

find;

END.

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<pre>

 

=={{header|Perl}}==

 

use strict; # https://rosettacode.org/wiki/Bioinformatics/global_alignment

use Data::Dump 'dd'; dd \%ch;

}

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<pre>

 

=={{header|Phix}}==

<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: #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>

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(Shows three length-6 results for the first test)

{{trans|Go}}

 

 

from collections import Counter

#

# .. if you don't want all possible shortest superstrings.

 

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{{trans|Go}}

{{trans|Julia}}

 

sub printCounts(\seq) {

>,

)

 

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{{libheader|Wren-str}}

{{libheader|Wren-math}}

import "/seq" for Lst

import "/str" for Str

var scs = shortestCommonSuperstring.call(test)

printCounts.call(scs)

 

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