trouble writing stored data to output

This is a discussion on trouble writing stored data to output within the C Programming forums, part of the General Programming Boards category; I am having trouble writing data to an output file. I am able to create the file but not able ...

  1. #1
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    trouble writing stored data to output

    I am having trouble writing data to an output file. I am able to create the file but not able to put anything in it.

    Heres the relevant code:

    Code:
    else if ((strcmp ( command, "write")) == 0 )
                        {
                            
                            list_num = atoi(strtok(NULL, " \n\t")) ;
                            filename = strtok(NULL, " \n\t") ;
                            output = fopen(filename, "w") ;
                            
                            fputs(loadedSequences[list_num].header, output) ;
                            fputs(loadedSequences[list_num].data, output) ;
                            
                            fclose(output) ;
                        }
    The command will look like the following:
    SeqTool> write # <filename>

    Any help would be great.
    Last edited by gkoenig; 03-30-2008 at 02:54 PM.

  2. #2
    and the Hat of Guessing tabstop's Avatar
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    You should check that fopen didn't fail (if it did, output == NULL). list_num looks like it should be the right thing. Do you have data in loadedSequences[list_num]? What are you getting?

  3. #3
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    here is more code to show what i am doing

    Code:
    #include <stdio.h>
    #include <string.h>
    #include <ctype.h>
    #include <stdlib.h>
    
    typedef struct { char *name ; char data[1000000] ; int length ; int type ; char header[1000] ; } sequence ;
    
    sequence loadedSequences[1000] ;
    
    int nSequences = 0 ;
        
    int main()
        {
            char std_input[1000] ;  // prev. buffer
            char header_data[1000] ;
            char seq_data[100000] ;
            char buffer[100000] ;
            char header_line[1000] ;
            
            FILE *input, *output ;
            
            char *seqName ;        
            char *command ;
            char *filename ;
            char *accession_id ;
        
            int list_num ;
            
            int i ;
            int c ;
            int n ;
            
            for(;;)
                {
                    printf("SeqTool> ") ;
                    
                    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( filename ) 
                                { 
                                    input = fopen(filename, "r") ;
                                    if ( !input )
                                        {
                                            perror(filename);
                                            continue ;
                                        }                                
                                }                            
                           
                            fgets( header_data, 1000, input) ; 
                                                    
                            seqName = &header_data[1] ;   // After the > in FASTA format
                            
                            strcpy( header_line, seqName ) ;  
                            
                            accession_id = strtok(header_line, " \n\t" ) ;
                           
                            loadedSequences[nSequences].name = 
                                (char *) malloc( ( strlen(accession_id) + 1 ) * sizeof( char ) ) ;
                                
                           
                           strcpy(loadedSequences[nSequences].header, seqName) ;
                           
                            
                           strcpy( loadedSequences[nSequences].name , accession_id ) ; 
                            
                            // Collect the sequence from FASTA file                                             
                            
                            n = 0 ;
                                                
                            while ((c = getc(input)) != EOF)
                                        {
                                            if(c >= 'A' && c <= 'Z')
                                                {
                                                    loadedSequences[nSequences].data[n++] = c ;
                                                 
                                                }
                                        }  
                                       
                            
                            loadedSequences[nSequences].length = strlen((loadedSequences[nSequences].data)) ;
                            
                            fclose(input) ;
                            
                            ++nSequences ;
                   
                        }
                        
    ///////////////// Write sequence in FASTA format //////////////////////////
                   
                    else if ((strcmp ( command, "write")) == 0 )
                        {
                            
                            list_num = atoi(strtok(NULL, " \n\t")) ;
                            filename = strtok(NULL, " \n\t") ;
                            output = fopen(filename, "w") ;
                            
                            fputs(loadedSequences[list_num].header, output) ;
                            fputs(loadedSequences[list_num].data, output) ;
                            
                            fclose(output) ;
                        }
    what i am trying to do is take the data that was read in from a file and stored, and write out to a different file. the data is stored in loadedSequences[nSequences].data and loadedSequences[nSequences].header

  4. #4
    and the Hat of Guessing tabstop's Avatar
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    There's nothing wrong with the fputs calls, provided the output file is opened and list_num is valid and there is data in the .header and .data strings. Are you sure that all those are true?

  5. #5
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    Thanks. My mistake was my index number. It should have been:

    Code:
    fputs(loadedSequences[list_num-1].header, output) ;
                            fputs(loadedSequences[list_num-1].data, output) ;

    Appreciate the help

  6. #6
    and the hat of wrongness Salem's Avatar
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    Code:
    typedef struct { char *name ; char data[1000000] ; int length ; int type ; char header[1000] ; } sequence ;
    
    sequence loadedSequences[1000] ;
    sizeof( loadedSequences ) is well over 1GB, you really need a different approach which involves say allocating data at run-time.
    If you dance barefoot on the broken glass of undefined behaviour, you've got to expect the occasional cut.
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