Converts a DNA sequence in a binary file

dna_bit.c

// Compile: gcc -o dna2bit dna_bit.c

// Libraries
#include <stdio.h>
#include <string.h>

// Declare constants
#define A 0 // 00
#define C 1 // 01
#define G 2 // 10
#define T 3 // 11
#define BYTES_PER_BATCH 1

// Declare headers and structs
struct Nucleotid translate(char c);
struct Nucleotid { unsigned int base: 2; };

// Main function
// It receives as argument the path to save the dna and the sequence in the next format:
// ./dna_bit path/to/file.dna GATATATACAGGTACA
int main(int argc, char** params) {
  FILE *write_ptr;
  char* pathToFile = params[1];
  char* sequence = params[2];

  printf("Welcome to DNA2Bit version 0.0.1\n");
  printf("Input sequence: %s \n", sequence);

  write_ptr = fopen(pathToFile, "wb");

  // Declare and first initialization of buffer variables:
  unsigned int buffer = 0;
  unsigned int basesInBufferCounter = 0;
  unsigned int bytesWritten = 0;

  // Iterate the sequence of chars
  for (int baseCounter = 0; baseCounter < strlen(sequence); ++baseCounter) {
    // Translate the char to the binary code
    struct Nucleotid nucleotid = translate(sequence[baseCounter]);

    // Puts the binary in the buffer and increments the counter
    buffer = (buffer << 2) | nucleotid.base;
    basesInBufferCounter++;

    if (basesInBufferCounter == 4) {
      // Write the 4 bases in the file (Write a byte)
      fwrite(&buffer, BYTES_PER_BATCH, BYTES_PER_BATCH, write_ptr);

      // Clean buffer variables
      basesInBufferCounter = 0;
      buffer = 0;
      bytesWritten++;
    }
  }

  // Closes the file and exit successfuly
  fclose(write_ptr);

  // Print statistics
  printf("Total nucleotids written: %d\n", (int)strlen(sequence));
  printf("Total bytes written: %d\n", bytesWritten);
  printf("File written in: %s\n", pathToFile);

  return 0;
}

struct Nucleotid translate(char base) {
  struct Nucleotid nucleotid;

  if (base == 'A' || base == 'a') {
    nucleotid.base = A;
  } else if (base == 'C' || base == 'c') {
    nucleotid.base = C;
  } else if (base == 'G' || base == 'g') {
    nucleotid.base = G;
  } else {
    nucleotid.base = T;
  }

  return nucleotid;
}