84 lines
2.0 KiB
C
84 lines
2.0 KiB
C
#include <stdio.h>
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#include <stdlib.h>
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int main ( int argc, char** args ){
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/*
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* About this program:
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* Reads a genome file and checks if its contents is valid.
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* If the content is invalid the program exits with -1 otherwise the program exits with 0
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*/
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if( argc != 2){
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printf("Program use: ./a.out <filePath>");
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} else {
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printf("Argument 1 : %s\n", args[1]);
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FILE* genomeFile = fopen(args[1], "r" );
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/*
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* File specification/requirements
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* The file must contain:
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* - 500 lines of 100 character plus the newline character
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* - each line of 100 character only contains characters A, C, G or T
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*/
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// PSUEDO Code
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// Step 1: Read the amount of bytes 101 characters take.
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// step 2: for the first 100 characters check if equal to A, C, G or T
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// step 3: If not okay close file and program exits (-1)
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// step 4: if okay check if the last byte is a newline
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// step 5: if not okay close file and program exits (-1)
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// step 6: if okay close file and program exits (0)
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const int LINESIZE = 101;
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unsigned int A = 0, G = 0, C = 0, T = 0;
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printf("start count: %i , %i , %i , %i\n" , A, C, G, T);
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for ( int i = 0; i < 500 ; i++){
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char line[LINESIZE];
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int bytesRead = fread(line, sizeof *line, LINESIZE, genomeFile);
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if( bytesRead != LINESIZE ){
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printf("Could only read %i bytes", bytesRead);
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goto FAILURE;
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}
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for ( int j = 0; j < 100; j++ ) {
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if( line[j] == 'A') {
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A ++;
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continue;
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}
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if( line[j] == 'C' ) {
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C ++;
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continue;
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}
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if( line[j] == 'G' ){
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G ++;
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continue;
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}
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if( line[j] == 'T' ) {
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T ++;
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continue;
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}
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printf("line %i character %i: %s is not valid.",i,j,line[j]);
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goto FAILURE;
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}
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if( line[100] != '\n') {
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printf("Read %c instead of newline ", line[100]);
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goto FAILURE;
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}
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}
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fclose (genomeFile);
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printf("Counted A's %i\nCounted C's %i\nCounted G's %i\nCounted T's %i\n" ,A ,C ,G ,T);
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exit(0);
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FAILURE:
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fclose(genomeFile);
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exit(-1);
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}
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}
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