src/hg/protein/spOrganism/spOrganism.c 1.4

Index: src/hg/protein/spOrganism/spOrganism.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/protein/spOrganism/spOrganism.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 1000000 -r1.3 -r1.4
--- src/hg/protein/spOrganism/spOrganism.c	28 Feb 2006 00:57:59 -0000	1.3
+++ src/hg/protein/spOrganism/spOrganism.c	23 Sep 2009 18:42:25 -0000	1.4
@@ -1,109 +1,109 @@
 /* spOrganism - Produce a .tab file of SWISS-PROT display ID/NCBI taxonomy ID pairs */
 #include "common.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "spOrganism - Extract taxonomy data from SWISS-PROT data file and \n"
   " produce a .tab file of SWISS-PROT display ID/NCBI taxonomy ID pairs.\n" 
   "usage:\n"
   "   spOrganism xxxx\n"
   "      xxxx is the input  file name\n"
   "      yyyy is the output file name\n"
   "example: spOrganism /cluster/store5/swissprot/070403/sprot.dat oxSP.tab\n");
 }
 
 int main(int argc, char *argv[])
 {
 char *id;
 char *ox;
 char *chp;
 char *infName, *outfName;
 
 char line[2000];
 FILE *inf, *outf;
 
 if (argc!=3)
    {
    usage();
    }
 
 infName  = argv[1];
 outfName = argv[2];
 
 if ((inf = fopen(infName, "r")) == NULL)
     {		
     fprintf(stderr, "Can't open file %s.\n", infName);
     exit(8);
     }
 
 outf = fopen(outfName, "w");
 
 while (fgets(line, 1000, inf) != NULL)
     {
     chp = strstr(line, "ID   ");
     if (chp != line)
 	{
 	fprintf(stderr, "expected ID line, but got: %s\n", line);
 	exit(1);
 	} 
     chp = chp + strlen("ID   ");
     id = chp;
     chp = strstr(id, " ");
     *chp = '\0';
     id = strdup(id);
 
     again:
     if (fgets(line, 1000, inf) == NULL) break;
 
     /* "//" is the end of record line */	
     if ((line[0] == '/') && (line[1] == '/')) goto one_done;
 
     chp = strstr(line, "OX   ");
     if (chp != NULL)
 	{
 	chp = strstr(line, "NCBI_TaxID=");
 	ox  = chp + strlen("NCBI_TaxID=");
 
 	again1:
 	chp = strstr(ox, ",");
 	if (chp != NULL)
 	    {
 	    *chp='\0';
 	    while (*ox == ' ') ox++;
 	    fprintf(outf, "%s\t%s\n", id, ox);
  	    chp++;
 	    ox = chp;	
 	    if (*ox == '\n') 
 		{
-		fgets(line, 1000, inf);
+		mustGetLine(inf, line, sizeof(line));
 		chp = strstr(line, "OX   ");
 		if (chp == NULL)
 		    {
 		    fprintf(stderr, "no OX line after OX continuation line!\n");
 		    exit(1);
 	 	    }
 		ox  = line + strlen("OX   ");
 		goto again1;
 	    	}	
 	    }
         else
 	    {
 	    chp = strstr(ox, ";");
 	    if (chp != NULL)
 	    	{
 	    	*chp = '\0';
 	    	while (*ox == ' ') ox++;
 	    	fprintf(outf, "%s\t%s\n", id, ox);
 	    	ox = NULL;
 	    	}	
 		}
     	if (ox != NULL) goto again1;
     	}
     goto again;
     one_done: id = id;
     }
 fclose(outf);
 return 0;
 }