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Full Discussion: Reading a binary file in text or ASCII format
Top Forums Programming Reading a binary file in text or ASCII format Post 82877 by jim mcnamara on Wednesday 7th of September 2005 11:08:17 AM
Old 09-07-2005
This comes up all too often. Windows has text files. Unix does not. Unix is not Windows. In Unix a file is a file is a file. It's a bag of bytes. Period.

Because a standard C string uses ASCII zero (nul character) as the end of string, that data from files that contain nuls (in Windows these are binary files, in Unix they are just files) cannot be parsed as strings because the nuls confuse everything.

To the OP: try
Code:
od -c filename

to find out what is in the file. Then you will know if you can read it using standard string C calls like fgets(). Or if you will have to use fread().

After you've programmed for a while you tend to bypass fread and fgets, especially when you're dealing with large files that may contain interesting stuff.
This reads an entire file containing anything into a buffer:
Code:
#include <stddef.h>
#include <sys/types.h>
#include <unistd.h>
#include <fcntl.h>
#include <stdlib.h>
#include <stdio.h>
#include <sys/stat.h>
#include <errno.h>
#include <assert.h>

#define ck(x) \
if( (x) == (-1) ){ perror("");exit(EXIT_FAILURE);}

/* read a buffer from a file */
ssize_t readall(int fd, void *buf, size_t *bytes){
     ssize_t nread = 0, n=0;
     size_t nbyte = *bytes;

     do {
         if ((n = read(fd, &((char *)buf)[nread], nbyte - nread)) == -1) {
             if (errno == EINTR)
                 continue;
             else
                 return (-1);
         }
         if (n == 0)
             return nread;
         nread += n;
     } while (nread < nbyte);
     return nread;
}

/* read control */
void readfile(char *fname, char *buffer, size_t *size, mode_t *mode)
{
   int fd=0;   
   struct stat st;
   
   ck(fd=open(fname,O_RDONLY) );
   ck(fstat(fd,&st) );
   *size=st.st_size;   
   *mode=st.st_mode;
   buffer=calloc(1,*size+1);
   ck(readall(fd, buffer, size) );    
   ck(close(fd) );
}


int main(int argc, char *argv[])
{
   char *buffer=NULL;
   size_t size;
   mode_t mode;
 
   readfile(argv[1],buffer,&size,&mode);
   /* play with buffer here  */
   free(buffer);
   return 0;  
}

This User Gave Thanks to jim mcnamara For This Post:
figaro
 

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LEARN ABOUT DEBIAN

hmmconvert

hmmconvert(1)							   HMMER Manual 						     hmmconvert(1)

NAME

       hmmconvert - convert profile file to a HMMER format

SYNOPSIS

       hmmconvert [options] <hmmfile>

DESCRIPTION

       The hmmconvert utility converts an input profile file to different HMMER formats.

       By  default,  the input profile can be in any HMMER format, including old/obsolete formats from HMMER2, ASCII or binary; the output profile
       is a current HMMER3 ASCII format.

OPTIONS

       -h     Help; print a brief reminder of command line usage and all available options.

       -a     Output profiles in ASCII text format. This is the default.

       -b     Output profiles in binary format.

       -2     Output in legacy HMMER2 ASCII text format, in ls (glocal) mode. This allows HMMER3 models to be converted back to a close approxima-
	      tion of HMMER2, for comparative studies.

       --outfmt <s>
	      Output  in a HMMER3 ASCII text format other then the most current one.  Valid choices for <s> are 3/b or 3/a.  The current format is
	      3/b, and this is the default. There is a slightly different format 3/a that was used in some alpha test code.

SEE ALSO

       See hmmer(1) for a master man page with a list of all the individual man pages for programs in the HMMER package.

       For complete documentation, see the user guide that came  with  your  HMMER  distribution  (Userguide.pdf);  or	see  the  HMMER  web  page
       (@HMMER_URL@).

COPYRIGHT

       @HMMER_COPYRIGHT@
       p@HMMER_LICENSE@

       For  additional	information  on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER
       web page (@HMMER_URL@).

AUTHOR

       Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147 USA
       http://eddylab.org

       "

HMMER 
@HMMER_VERSION@						   @HMMER_DATE@ 						     hmmconvert(1)
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