Step by Step solution about How to resolve the algorithm Bioinformatics/base count step by step in the Kotlin programming language

Explanation:

This Kotlin code demonstrates data analysis on a DNA sequence using sequence processing functions. Here's a detailed breakdown:

1. printSequence Function:

• Defines a function printSequence that takes a DNA sequence and an optional width (default: 50).

2. Nested printWithLabel Function:

• Defines a nested function printWithLabel that takes a label and data and prints them with a consistent format.

3. Printing the Original Sequence:

• Prints the header "SEQUENCE:" and iterates over the sequence in chunks of the specified width.
• For each chunk, it prints the chunk and its start position in the sequence using printWithLabel.

4. Base Count Analysis:

• Prints the header "BASE:" and groups the sequence by each base (A, C, G, T) using groupingBy.
• For each group, it counts the occurrences and prints the base and the count using printWithLabel.

5. Total Count:

• Prints the total length of the sequence using printWithLabel.

6. Main Function:

• Sets a constant BASE_SEQUENCE with a long DNA sequence.
• Calls printSequence with the BASE_SEQUENCE as input.

Example Output:

SEQUENCE:
0: CGTAAAAAAAAA
50: TACAACGTCCTT
100: TGGCTATCTCT
150: TAAACTCCTGCT
200: AAATGCTCGTGC
250: TTTCCAATTATG
300: TAAGCGTTCCG
350: AGACGGGGTGG
400: TCGATTCTGAGG
450: ACAAAAGGTCA
500: AGATGGAGCGC
550: ATCGAACGCAA
600: TAAGGATCATTT
650: GATGGGACGTT
700: TCGTCGACAAA
750: GTCTTGTTTCCG
800: AGAGTAACGGCT
850: ACCGTCTTCGAT
900: TCTGCTTATAAC
950: ACTATGTTCTT
BASE:
A: 133
C: 193
G: 188
T: 186
TOTALS: 700

In this example, the code analyzes the BASE_SEQUENCE and prints the original sequence in chunks of 50 characters. It also provides a breakdown of the base counts and the total length of the sequence.

fun printSequence(sequence: String, width: Int = 50) {

    fun printWithLabel(label: Any, data: Any) =
        label.toString().padStart(5).also { println("$it: $data") }

    println("SEQUENCE:")
    sequence.chunked(width).forEachIndexed() { i, chunk ->
        printWithLabel(i * width + chunk.length, chunk)
    }

    println("BASE:")
    sequence.groupingBy { it }.eachCount().forEach { (k, v) ->
        printWithLabel(k, v)
    }
    printWithLabel("TOTALS", sequence.length)
}

const val BASE_SEQUENCE = "CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATATTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTATCGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTGTCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGACGACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT"

fun main() = printSequence(BASE_SEQUENCE)