4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/makeDb/outside/hgBioCyc/hgBioCyc.c src/hg/makeDb/outside/hgBioCyc/hgBioCyc.c
index 2ad09f4..08c040e 100644
--- src/hg/makeDb/outside/hgBioCyc/hgBioCyc.c
+++ src/hg/makeDb/outside/hgBioCyc/hgBioCyc.c
@@ -1,94 +1,94 @@
 /* hgBioCyc - Creates bioCycPathway.tab for Known Genes to link to SRI BioCyc pathways */
 
 /* Copyright (C) 2013 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #include "common.h"
 #include "hCommon.h"
 #include "hdb.h"
 
 FILE *inf;
 char line_in[10000];
 char line[10000];
 char *infileName;
 
 int aaLen;
 int cdsLen;
 char cond_str[256];
 char *aaStr;
 
 void usage()
 /* Explain usage and exit. */
 {   
 errAbort(
   "bioCyc - Creates bioCycPathway.tab for Known Genes to link to SRI BioCyc pathways\n"
   "usage:\n"
   "   hgBoCyc xxxx yyyy\n"
   "      xxxx is the input file name\n"
   "      yyyy is the genome under construction\n"
   "example:\n"
   "   hgBioCyc gene-pathway.dat hg16\n");
 }
     
 int main(int argc, char *argv[])
 {
 FILE *o1;
 char *chp;
 char *genomeDBname;
 char refseqID[40], mapID[40];
 char *kgID, *geneSymbol;
  
 if (argc != 3) usage();
   
 infileName      = argv[1];
 genomeDBname    = argv[2];
 
 o1 = fopen("j.dat", "w");
 
 inf  = mustOpen(infileName, "r");
 while (fgets(line_in, 1000, inf) != NULL)
     {
     strcpy(line, line_in);
     chp = strstr(line, "\t");
     *chp = '\0';
     strcpy(refseqID, line);
 
 again:
     chp ++;
     chp = strtok(chp, "\r\t\n");	
 
     if (chp == NULL) continue;
 
     sqlSafefFrag(cond_str, sizeof cond_str, "alias='%s'", refseqID);
     kgID=sqlGetField(genomeDBname, "kgAlias", "kgID", cond_str);
 
     // check with refLink if not found in kgAlias
     if (kgID == NULL)
 	{
     	sqlSafefFrag(cond_str, sizeof cond_str, "mrnaAcc='%s'", refseqID);
     	geneSymbol=sqlGetField(genomeDBname, "refLink", "name", cond_str);
     	sqlSafefFrag(cond_str, sizeof cond_str, "alias='%s'", geneSymbol);
     	kgID=sqlGetField(genomeDBname, "kgAlias", "kgID", cond_str);
 	}
 
     strcpy(mapID, chp);
    
     if (kgID != NULL)
 	{ 
     	fprintf(o1, "%s\t%s\t%s\n", kgID, refseqID, mapID);fflush(stdout);
     	}
     else
 	{
 	printf("%s not found in kgAlias nor in refLink\n", refseqID);
 	}
     chp = chp + strlen(mapID);
     
     // process remaing refeqID(s)
     goto again;
     }
 
 fclose(o1);
 mustSystem("cat j.dat|sort|uniq >bioCycPathway.tab");
 mustSystem("rm j.dat");
 return 0;
 }