Bioinformatics/Sequence mutation: Difference between revisions

<p>

This example use a <code>List</code> to hold the base values.<br />

The <code>Random</code> class is used to generate random integer values.<br />

A <code>record</code> is used to hold the counts of each base.

</p>

<p>

The "pretty print" is defined within the <code>toString</code> method.<br />

Which uses a <code>StringBuilder</code> to generate a <kbd>string</kbd> of sequential bases.<br />

A <code>BufferedReader</code> to read the augmented <kbd>string</kbd> line-for-line.<br />

Finally, a <kbd>string</kbd> formatter is used to justify and format the output text.

</p>

<syntaxhighlight lang="java">

import java.io.BufferedReader;

import java.io.IOException;

import java.io.StringReader;

import java.util.ArrayList;

import java.util.List;

import java.util.Random;

class Program {

List<Character> sequence;

Random random;

SequenceMutation() {

sequence = new ArrayList<>();

random = new Random();

}

void generate(int amount) {

for (int count = 0; count < amount; count++)

sequence.add(randomBase());

}

void mutate(int amount) {

int index;

for (int count = 0; count < amount; count++) {

index = random.nextInt(0, sequence.size());

switch (random.nextInt(0, 3)) {

case 0 -> sequence.set(index, randomBase());

case 1 -> sequence.remove(index);

case 2 -> sequence.add(index, randomBase());

}

}

}

private char randomBase() {

return switch (random.nextInt(0, 4)) {

case 0 -> 'A';

case 1 -> 'C';

case 2 -> 'G';

case 3 -> 'T';

default -> '?';

};

}

private Base count(String string) {

int a = 0, c = 0, g = 0, t = 0;

for (char base : string.toCharArray()) {

switch (base) {

case 'A' -> a++;

case 'C' -> c++;

case 'G' -> g++;

case 'T' -> t++;

}

}

return new Base(a, c, g, t);

}

/* used exclusively for count totals */

private record Base(int a, int c, int g, int t) {

int total() {

return a + c + g + t;

}

@Override

public String toString() {

return "[A %2d, C %2d, G %2d, T %2d]".formatted(a, c, g, t);

}

}

@Override

public String toString() {

StringBuilder string = new StringBuilder();

StringBuilder stringB = new StringBuilder();

String newline = System.lineSeparator();

for (int index = 0; index < sequence.size(); index++) {

if (index != 0 && index % 50 == 0)

string.append(newline);

string.append(sequence.get(index));

stringB.append(sequence.get(index));

}

try {

BufferedReader reader = new BufferedReader(new StringReader(string.toString()));

string = new StringBuilder();

int count = 0;

String line;

while ((line = reader.readLine()) != null) {

string.append(count++);

string.append(" %-50s ".formatted(line));

string.append(count(line));

string.append(newline);

}

} catch (IOException exception) {

/* ignore */

}

string.append(newline);

Base bases = count(stringB.toString());

int total = bases.total();

string.append("Total of %d bases%n".formatted(total));

string.append("A %3d (%.2f%%)%n".formatted(bases.a, ((double) bases.a / total) * 100));

string.append("C %3d (%.2f%%)%n".formatted(bases.c, ((double) bases.c / total) * 100));

string.append("G %3d (%.2f%%)%n".formatted(bases.g, ((double) bases.g / total) * 100));

string.append("T %3d (%.2f%%)%n".formatted(bases.t, ((double) bases.t / total) * 100));

return string.toString();

}

}

</syntaxhighlight>

<p>

Here is a sequence of 200 mutated 10 times.

</p>

<pre>

Before mutation

0 TCGCTTGGGGGGAGCAAGGTGTTCGCAATAGATCACAGCCGGTCTCGCAT [A 10, C 12, G 17, T 11]

1 AGCTATTTCTACGCTATCGAGCCTGTACTGTGTCAGTAGACCATGTACTC [A 11, C 13, G 10, T 16]

2 CCCAGACTCGTCTTGCCAAGTGACTGCTCAAGGGGAGCGCCCACAGGGTA [A 11, C 16, G 15, T 8]

3 TCTAGAGCATTCGATCACACGGAAAAATTTTATTCGGCAGATCCAGTTAA [A 17, C 10, G 9, T 14]

Total of 200 bases

A 49 (24.50%)

C 51 (25.50%)

G 51 (25.50%)

T 49 (24.50%)

After mutation

0 TCGCTTGGGGGGAGTAAGGTGTTCGCAATAGTCACAGCCGGTCTCGCATA [A 10, C 11, G 17, T 12]

1 GCTTTTCTACGCATCGAGCCTGTACTGTGTCAGTAGACATGTACTCCCCA [A 10, C 15, G 10, T 15]

2 GACTCGTTTGCCAAGTGACCTGCTCAAGGGGAGCGCCCACAGGGTACTAG [A 11, C 14, G 16, T 9]

3 AGCAGTTCGATCACACGGAAAAATTTTTTCGGCAGATCCAGTTAA [A 15, C 9, G 9, T 12]

Total of 195 bases

A 46 (23.59%)

C 49 (25.13%)

G 52 (26.67%)

T 48 (24.62%)

</pre>

<p>

Here is a sequence of 200 mutated 90,000 times

</p>

<pre>

Before mutation

0 CGCACCCTCCTTCGGGCGAAGCGGGGTTATTTACCCGATTCACCGCACCT [A 8, C 19, G 12, T 11]

1 CGCGGCTCTAAAAGTTCGAAGATCCCTGCGTAGACTGGACCTCATAACAA [A 15, C 14, G 11, T 10]

2 CCGTATTACGCTCCGTACGAATAACTCGGTTGTGCGATGCGGAAAGCGAC [A 12, C 13, G 14, T 11]

3 ATTTCTCAGGCCGAACGTACGCTTCTCTCCTACACCTCGCCTCGAGTATG [A 9, C 18, G 9, T 14]

Total of 200 bases

A 44 (22.00%)

C 64 (32.00%)

G 46 (23.00%)

T 46 (23.00%)

After mutation

0 CGTTTAAGCGGGAAGGTCGTCCACCACACGAAGGCCCCCCTCCAGCACTA [A 12, C 19, G 12, T 7]

1 CCCTGGGCGAGTGCGACCGGCTACAAGAATACGGACAACCGCACTTCGTA [A 13, C 16, G 14, T 7]

2 GTTGCGACGCCAAACCGAGGTTTGAAAGGCAGCCGAAACTCCTAGCCATC [A 14, C 15, G 13, T 8]

3 CGGGCAGCCCACTGGTTTAGATGTTACGTGATGGAAAGGTGGATCATCGT [A 11, C 9, G 17, T 13]

4 GGTTGCCCTGGCGTTGCGTACTTCGTGTCTGAATATTGGTTACAATCGCT [A 7, C 11, G 14, T 18]

5 CGACGACCTGACGATTCTGGATCAACCAACTGCCTAAAGTCGCGAATTAA [A 16, C 14, G 10, T 10]

6 TAATCGACTGCATCACATGTTAGTCTAGTCATCACGAGTACATAGTGTGG [A 14, C 10, G 11, T 15]

7 CCACCTCCTAACGTACTATTTACATAGGATATGGCAGCCCTAACGCACAC [A 15, C 17, G 7, T 11]

8 TGTACGAAAGTGAGACTCCTTACCGAGATTCTAGGCTTAGTGATCCTTGA [A 13, C 10, G 12, T 15]

9 AAACGCTAGCCTAGGAATGACGGGGACTTGATCGGCC [A 10, C 9, G 12, T 6]

Total of 487 bases

A 125 (25.67%)

C 130 (26.69%)

G 122 (25.05%)

T 110 (22.59%)

</pre>

<br />

Here is an alternate demonstration