Bioinformatics/Sequence mutation: Difference between revisions
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</pre>
=={{header|Mathematica}} / {{header|Wolfram Language}}==
BioSequence is a fundamental data type in Mathematica:
<lang Mathematica>SeedRandom[13122345];
seq = BioSequence["DNA", "ATAAACGTACGTTTTTAGGCT"];
randompos = RandomInteger[seq["SequenceLength"]];
seq = StringReplacePart[seq, RandomChoice[{"A", "T", "C", "G"}], {randompos, randompos}];
randompos = RandomInteger[seq["SequenceLength"]];
seq = StringReplacePart[seq, "", {randompos, randompos}];
randompos = RandomInteger[seq["SequenceLength"]];
seq = StringInsert[seq, RandomChoice[{"A", "T", "C", "G"}], randompos];
seq = BioSequence["DNA", StringJoin@RandomChoice[{"A", "T", "C", "G"}, 250]];
size = 50;
parts = StringPartition[seq["SequenceString"], UpTo[size]];
begins = Most[Accumulate[Prepend[StringLength /@ parts, 1]]];
ends = Rest[Accumulate[Prepend[StringLength /@ parts, 0]]];
StringRiffle[MapThread[ToString[#1] <> "-" <> ToString[#2] <> ": " <> #3 &, {begins, ends, parts}], "\n"]
Tally[Characters[seq["SequenceString"]]]
Do[
type = RandomChoice[{1, 2, 3}];
Switch[type, 1,
randompos = RandomInteger[seq["SequenceLength"]];
seq = StringReplacePart[seq, RandomChoice[{"A", "T", "C", "G"}], {randompos, randompos}];
, 2,
randompos = RandomInteger[seq["SequenceLength"]];
seq = StringReplacePart[seq, "", {randompos, randompos}];
, 3,
randompos = RandomInteger[seq["SequenceLength"]];
seq = StringInsert[seq, RandomChoice[{"A", "T", "C", "G"}], randompos];
]
,
{10}
]
parts = StringPartition[seq["SequenceString"], UpTo[size]];
begins = Most[Accumulate[Prepend[StringLength /@ parts, 1]]];
ends = Rest[Accumulate[Prepend[StringLength /@ parts, 0]]];
StringRiffle[MapThread[ToString[#1] <> "-" <> ToString[#2] <> ": " <> #3 &, {begins, ends, parts}], "\n"]
Tally[Characters[seq["SequenceString"]]]</lang>
{{out}}
<pre>1-50: TAGCAGGGGAATTGTCGACTCCCGGGTTTCAATTGCCAACCAAGCATATT
51-100: GTACGCTCGTTCATTATAGGGGAAATGCGAGGGGCTAGAACGTTAGCTTC
101-150: GAGAGGTCGCGGCAATTTAGGGGGGCACCAAACGGTTTATAATACAGGGA
151-200: CTGATACATTCGCTGGAAAACAATTCTGCCCAGCAGCGACTCCGGACAAC
201-250: GTGACTTTGGTCCAAGATATTAGATTATCAATCCGTATTAATGTAGGCTT
{{"T", 63}, {"A", 69}, {"G", 66}, {"C", 52}}
1-50: TAGCAGGGGAATTGTCGACTCCCGGGTTCAATTGCCAACCAAGATATTGT
51-100: ACGCTCGTTCATTATAGGGGAAATGCGAGGGGCTAGAAACGTTAGTTCGA
101-150: GAGGTCGCGGAAATTTAGGGGGGCACCAACGGTTTATAATACAGGGACTG
151-200: ATACATTCGCTGGAAAACAATTCTGCCCAGCAGCGACTCCGGACAACGTG
201-246: ACTTTGGTCCAAGATAGTTAGATATCAATCCGTATAATGTAGGCTT
{{"T", 60}, {"A", 70}, {"G", 67}, {"C", 49}}</pre>
=={{header|Nim}}==
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