Thread: Bus error when reading input from file

Hello to all,

I am receiving a bus error when I run the following code:

Code:

#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include <stdlib.h>

typedef struct { char *name ; char *data ; int length ; int type ; } sequence ;

sequence loadedSequences[1000] ;

int nSequences = 0 ;
    
int main()
    {
        char buffer[1000] ;        
        char *command ;
        char *filename, *list_num ;
        
        
        for(;;)
            {
                printf("SeqTool> ") ;
                fpurge(stdin) ;
                
                fgets(buffer, 1000, stdin) ;
                fpurge(stdin) ;
                
                // Eliminating the newline character
                char *p = strchr(buffer, '\n') ;
                if (p) 
                    {
                        *p = '\0' ; 
                    } 
                                          
                command = strtok( buffer, " \t\n" ) ; 
                
////////////////// Load sequence in FASTA format //////////////////////////
                
                if( (strcmp ( command, "read" )) == 0 )
                    {
                        char *fileName ;
                        fileName = strtok(NULL, " \t\n" ) ;
                        FILE *input = fopen(filename, "r") ;
                        fgets( buffer, 1000, input) ;
                        char *seqName ;
                        seqName = &buffer[1] ;   // After the > in FASTA format  
                        
                        loadedSequences[nSequences].name = 
                            (char *) malloc( ( strlen(seqName) + 1 ) * sizeof( char ) ) ;
                            
                        strcpy( loadedSequences[nSequences].name , seqName ) ;
                        
                        ++nSequences ;
               
                    }

What I am trying to do is read in from a standardized format (FASTA) and collect the data so that I can manipulate it later if needed. The syntax for the command should be:

SeqTool> read <filename>

Any help would be great.

You're also creating variables in the middle of your code, variables that have an eerily similar name to something that you've already defined at the top of your main(). That might not be your problem, either, but it would certainly lead to confusion for me if this was my program.

I now have a new problem.

I want to set a condition so that if my input file doesn't exist, it will print an error message. As of now I am getting a "bus error". However, if i read in a file that exist, I get no problems.
Here is the code:

Code:

for(;;)
            {
                printf("SeqTool> ") ;
                fpurge(stdin) ;
                
                fgets(std_input, 1000, stdin) ;
                fpurge(stdin) ;
                
                // Eliminating the newline character
                char *p = strchr(std_input, '\n') ;
                if (p) 
                    {
                        *p = '\0' ; 
                    } 
                                          
                command = strtok( std_input, " \t\n" ) ; 
                
////////////////// Load sequence in FASTA format //////////////////////////
                
                if( (strcmp ( command, "read" )) == 0 )
                    {
                        
                        filename = strtok(NULL, " \t\n" ) ; // collect filename
                        
                        if( ! (input = fopen(filename, "r"))) 
                            { 
                                printf("COULD NOT OPEN FILE") ;
                            }
                       
               
                    }

The format for the command should look like this:
SeqTool> read <filename>

Any help would be great

Thanks for the help. Running fine.