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/kgProtAlias/kgProtAlias.c src/hg/protein/kgProtAlias/kgProtAlias.c
index 9103869..7e69180 100644
--- src/hg/protein/kgProtAlias/kgProtAlias.c
+++ src/hg/protein/kgProtAlias/kgProtAlias.c
@@ -1,125 +1,125 @@
 /* kgProtAlias - generate protein alias list table */
 
 /* 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(
   "kgProtAlias - create protein alias .tab files "
   "usage:\n"
   "   kgProtAlias xxxx yyyy\n"
   "            xxxx is genome  database name\n"
   "            yyyy is protein database date \n"
   "example: kgProtAlias hg16 040315\n");
 }
 
 int main(int argc, char *argv[])
     {
     struct sqlConnection *conn, *conn2;
     char query[256], query2[256];
     struct sqlResult *sr, *sr2;
     char **row, **row2;
 
     char *kgID;
     FILE *o1;
 
     char cond_str[256];
     char *database;
     char spDB[256];
     char proteinDB[256];
 
     char *chp;
 
     char *alignID;
     char *displayID, *secondaryID, *pdbID;
     char *proteinAC;
     char *ncbiProtAc;
 
     if (argc != 3) usage();
     database  = cloneString(argv[1]);
     
     sprintf(spDB, "sp%s", argv[2]);
     sprintf(proteinDB, "proteins%s", argv[2]);
 
     conn = hAllocConn(database);
     conn2= hAllocConn(database);
 
     o1 = fopen("j.dat", "w");
 
     sqlSafef(query2, sizeof query2, "select name, proteinID, alignID from %s.knownGene;", database);
     
     sr2 = sqlMustGetResult(conn2, query2);
     row2 = sqlNextRow(sr2);
     while (row2 != NULL)
 	{
 	kgID		= row2[0];
 	displayID	= row2[1];
 	alignID		= row2[2];
 
 	fprintf(o1, "%s\t%s\t%s\n", kgID, displayID, displayID);
        
         sqlSafefFrag(cond_str, sizeof cond_str, "displayID = '%s'", displayID);
         proteinAC = sqlGetField(proteinDB, "spXref3", "accession", cond_str);
         if (proteinAC != NULL)
 		{
 		fprintf(o1, "%s\t%s\t%s\n", kgID, displayID, proteinAC);
         
 		sqlSafefFrag(cond_str, sizeof cond_str, "acc = '%s' and extDb=1", proteinAC);
         	ncbiProtAc = sqlGetField(spDB, "extDbRef", "extAcc2", cond_str);
 		if (ncbiProtAc != NULL)
 		    {
 		    chp = strstr(ncbiProtAc, ".");
 		    if (chp != NULL) *chp = '\0';
 		    fprintf(o1, "%s\t%s\t%s\n", kgID, displayID, ncbiProtAc);
 		    }
 		}
 	else
 		{
 		fprintf(stderr, "%s\t%s\t%s does not have protein accession number!\n", 
 			kgID, displayID, alignID);
 		fflush(stderr);
 		break;
 		}
  
 	sqlSafef(query, sizeof query,"select accession2 from %s.spSecondaryID where displayID='%s';", 
 		proteinDB, displayID);
     	sr = sqlMustGetResult(conn, query);
     	row = sqlNextRow(sr);
     	while (row != NULL)
 		{
 		secondaryID = row[0];
 		fprintf(o1, "%s\t%s\t%s\n", kgID, displayID, secondaryID);
 		row = sqlNextRow(sr);
 		}
     	sqlFreeResult(&sr);
 
         sqlSafef(query, sizeof query,"select pdb from %s.pdbSP where sp='%s';", proteinDB, displayID);
     	sr = sqlMustGetResult(conn, query);
     	row = sqlNextRow(sr);
     	while (row != NULL)
 		{
 		pdbID = row[0];
 		fprintf(o1, "%s\t%s\t%s\n", kgID, displayID, pdbID);
 		row = sqlNextRow(sr);
 		}
     	sqlFreeResult(&sr);
 	fflush(o1);
    
 	row2 = sqlNextRow(sr2);
 	}
     sqlFreeResult(&sr2);
 
     fclose(o1);
     hFreeConn(&conn);
     hFreeConn(&conn2);
 
     mustSystem("cat j.dat|sort|uniq  >kgProtAlias.tab");
     mustSystem("rm j.dat");
     
     return(0);
     }