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/kgProtAliasNCBI/kgProtAliasNCBI.c src/hg/protein/kgProtAliasNCBI/kgProtAliasNCBI.c
index 970f9ee..2dc47bc 100644
--- src/hg/protein/kgProtAliasNCBI/kgProtAliasNCBI.c
+++ src/hg/protein/kgProtAliasNCBI/kgProtAliasNCBI.c
@@ -1,114 +1,114 @@
 /* kgProtAliasNCBI - generate alias list table for NCBI protein AC */
 
 /* 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(
   "kgProtAliasNCBI - create gene alias (mRNA part) .tab files "
   "usage:\n"
   "   kgProtAliasNCBI <DB> <RO_DB>\n"
   "            <DB> is knownGene DB under construction\n"
   "            <RO_DB> is read only target genome database\n"
   "example: kgProtAliasNCBI kgDB hg16\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn, *conn2;
 
 char query[256], query2[256];
 struct sqlResult *sr, *sr2;
 char **row, **row2;
  
 char *chp;
 char *kgID;
 FILE *o2;
 char cond_str[256];
 char *database;
 char *ro_db;
 
 char *proteinID;
 char *proteinAC;
 
 if (argc != 3) usage();
 database  = cloneString(argv[1]);
 ro_db  = cloneString(argv[2]);
 
 conn = hAllocConn(database);
 conn2= hAllocConn(database);
 o2 = fopen("jj.dat", "w");
 
 sqlSafef(query2, sizeof query2, "select name, proteinID from %s.knownGene;", database);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     kgID = row2[0];
     proteinID = row2[1];
 
     // get RefSeq protein AC numbers (NP_xxxxx) if they exist
     sqlSafefFrag(cond_str, sizeof cond_str, "kgID='%s'", kgID);
     proteinAC = sqlGetField(database, "kgXref", "protAcc", cond_str);
     if (proteinAC != NULL)
 	{
 	if (strlen(proteinAC) > 0)
 	    {
 	    fprintf(o2, "%s\t%s\t%s\n", kgID, proteinID, proteinAC);
 	    }
 	}
 
     // get Genbank protein accession numbers
     if (strstr(kgID, "NM_") != NULL)
 	{
 	sqlSafef(query, sizeof query,"select protAcc from %s.refLink where mrnaAcc = '%s';", ro_db, kgID);
 	sr = sqlMustGetResult(conn, query);
 	row = sqlNextRow(sr);
 	while (row != NULL)
     	    {
     	    proteinAC = row[0];
 	    fprintf(o2, "%s\t%s\t%s\n", kgID, proteinID, proteinAC);
 	    row = sqlNextRow(sr);
 	    }
     	sqlFreeResult(&sr);
 	}
     else
 	{
 	sqlSafef(query, sizeof query,"select proteinAC from %sTemp.locus2Acc0 where gbAC like '%s%c';", database, kgID, '%');
 	sr = sqlMustGetResult(conn, query);
 	row = sqlNextRow(sr);
 	while (row != NULL)
     	    {
     	    proteinAC = row[0];
 
 	    chp = strstr(proteinAC, ".");
 	    if (chp != NULL)
 		{
 		*chp = '\0';
 		}
 	    if (proteinAC[0] != '-')
 		{
 		fprintf(o2, "%s\t%s\t%s\n", kgID, proteinID, proteinAC);
 		}
 	    row = sqlNextRow(sr);
 	    }
     	sqlFreeResult(&sr);
 	}
     row2 = sqlNextRow(sr2);
     }
 sqlFreeResult(&sr2);
 fclose(o2);
 hFreeConn(&conn);
 hFreeConn(&conn2);
 
 mustSystem("cat jj.dat|sort|uniq  >kgProtAliasNCBI.tab");
 mustSystem("rm jj.dat");
     
 return(0);
 }