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/protein/kgBioCyc0/kgBioCyc0.c src/hg/protein/kgBioCyc0/kgBioCyc0.c
index 7e8e1f6..eb2663c 100644
--- src/hg/protein/kgBioCyc0/kgBioCyc0.c
+++ src/hg/protein/kgBioCyc0/kgBioCyc0.c
@@ -1,123 +1,123 @@
 /* kgBioCyc0 - collect needed data from BioCyc database */
 
 /* 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"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "kgBioCyc0 - collect needed data from BioCyc database \n"
   "usage:\n"
   "   kgBioCyc0 bioCycDb gdb\n"
   "      bioCycDb is the BioCyc database\n"
   "      gdb is the genome database\n"
   "      ensDb is the genome database where ensemblXref3 resides\n"
   "example: kgBioCyc0 bioCyc060216 hg18 hg17\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn2, *conn3;
 char *pathway;
 
 char *gdb, *bioCycDb, *ensGdb;
 int i;
 char *geneId = NULL;
 char *symbol;
 
 char query2[256], query3[256];
 struct sqlResult *sr2, *sr3;
 char **row2, **row3;
 
 FILE   *outf;
 char *kgId;
 
 if (argc != 4) usage();
 bioCycDb = argv[1];
 gdb      = argv[2];
 ensGdb   = argv[3];
    
 outf = fopen("bioCycPathway.tmp", "w");
 conn2= hAllocConn(gdb);
 conn3= hAllocConn(gdb);
 	
 sqlSafef(query2, sizeof query2,  "select * from %s.pathways;", bioCycDb);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     pathway = row2[0];
     for (i=0; i<63; i++)
     	{
 	/* first get kgId of genes with the same gene symbol */
     	sqlSafef(query3, sizeof query3,  "select gene_name%d from %s.pathways where UNIQUE_ID='%s'", 
     	    i+1, bioCycDb, pathway);
 
     	sr3 = sqlMustGetResult(conn3, query3);
     	row3 = sqlNextRow(sr3);
 	
 	symbol = strdup(row3[0]);
     	sqlFreeResult(&sr3);
 	
 	if (strcmp(symbol, "") != 0)
 	    {
 	    sqlSafef(query3, sizeof query3,  "select kgId from %s.kgXref where geneSymbol = '%s'", gdb, symbol);
 
     	    sr3 = sqlMustGetResult(conn3, query3);
     	    row3 = sqlNextRow(sr3);
 
 	    if (row3 != NULL)
 	    	{
 	    	kgId= row3[0];
 	    	if (strcmp(kgId, "") != 0)
 	    	    {
 	    	    fprintf(outf, "%s\t%s\t%s\n", kgId, symbol, pathway);fflush(stdout);
 	    	    }
 	    	}
     	    sqlFreeResult(&sr3);
 	    }
 	/* then get kgIds with the same UniProt accession via Ensembl gene IDs */
 	sqlSafef(query3, sizeof query3,  "select gene_id%d from %s.pathways where UNIQUE_ID='%s'", 
     	    i+1, bioCycDb, pathway);
     	sr3 = sqlMustGetResult(conn3, query3);
     	row3 = sqlNextRow(sr3);
 	
 	geneId = NULL;
 	if (row3 != NULL) 
 	    if (row3[0] != NULL) geneId = cloneString(row3[0]);
     	sqlFreeResult(&sr3);
 	if (geneId != NULL) 
 	    if (strcmp(geneId, "") != 0)
 	    	{
             	sqlSafef(query3, sizeof(query3),
                       "select kgId from %s.kgXref k, %s.ensGeneXref e where e.gene_id='%s' and k.spId=e.external_name and external_db like 'UniProt%%'", 
                       gdb, ensGdb, geneId);
     	    	sr3 = sqlMustGetResult(conn3, query3);
     	    	row3 = sqlNextRow(sr3);
 	    	if (row3 != NULL)
 	    	    {
 	    	    kgId= row3[0];
 	    	    if (strcmp(kgId, "") != 0)
 	    	    	{
 	    	    	fprintf(outf, "%s\t%s\t%s\n", kgId, geneId, pathway);fflush(stdout);
 	    	    	}
 	    	    }
     	    	sqlFreeResult(&sr3);
 	    	}
 	}
     row2 = sqlNextRow(sr2);
     }
 sqlFreeResult(&sr2);
 hFreeConn(&conn2);
 hFreeConn(&conn3);
 fclose(outf);
 
 system("cat bioCycPathway.tmp |sort -u  >bioCycPathway.tab");
 system("rm bioCycPathway.tmp");
 return(0);
 }