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/kgPutBack/kgPutBack.c src/hg/protein/kgPutBack/kgPutBack.c
index 95aaba3..dfcc5b2 100644
--- src/hg/protein/kgPutBack/kgPutBack.c
+++ src/hg/protein/kgPutBack/kgPutBack.c
@@ -1,106 +1,106 @@
 /* kgPutBack - From the initial gene candidates, */
 /* go through various criteria on gene-check results and keep the ones that pass the criteria */
 
 /* 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(
   "kgPutBack - from gene candidates, go through various criteria and keep the ones that pass the criteria \n"
   "usage:\n"
   "   kgPutBack tempDb genomeDb protDb putBackTable outfile\n"
   "      tempDb is the temp KG DB name\n"
   "      genomeDb is the genome DB where refGene and mgcGenes tables are\n"
   "      protDb is the proteinsYYMMDD DB\n"
   "      putBackTable is the put back list table\n"
   "      outfile is the output file name\n"
   "example: kgPutBack kgHg18ATemp hg18 sp060115 kgPutBack2 kgPutBack2.gp\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn, *conn2, *conn3;
 char query2[256], query3[256], query[256];
 struct sqlResult *sr2, *sr3, *sr;
 char **row2, **row3, **row;
 int  icnt;
 char *proteinID;
 char *kgId;
 char *spDb;
 char *kgTempDb;
 char *outfileName;
 FILE *outf;
 int  i;
 
 char *genomeDb;
 int  iAlign = 0;
 
 char *putBackTable;
 
 if (argc != 6) usage();
 kgTempDb    = argv[1];
 genomeDb    = argv[2];
 spDb  = argv[3];
 putBackTable= argv[4];
 outfileName = argv[5];
 
 outf = mustOpen(outfileName, "w");
 conn = hAllocConn(genomeDb);
 conn2= hAllocConn(genomeDb);
 conn3= hAllocConn(genomeDb);
 
 icnt = 1;
 /* go through each put back RefSeq */
 sqlSafef(query2, sizeof(query2), "select distinct acc from %s.%s", kgTempDb, putBackTable);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     kgId = row2[0];
     
     sqlSafef(query3, sizeof(query3), 
           "select * from %s.refGene where name='%s'", genomeDb, kgId);
     sr3  = sqlMustGetResult(conn3, query3);
     row3 = sqlNextRow(sr3);
 	{
         sqlSafef(query, sizeof(query), 
             "select d.val,score from %s.protMrnaScore,%s.displayId d where mrnaAcc='%s' and d.acc=protAcc order by score desc",
 	    kgTempDb, spDb, kgId);
     	sr  = sqlMustGetResult(conn, query);
     	row = sqlNextRow(sr);
 	if (row != NULL)
 	    {
 	    proteinID = row[0];	    
 	
 	    for (i=0; i<10; i++) fprintf(outf, "%s\t", row3[i]);
 	    iAlign++;
 	    fprintf(outf, "%s\tR%dP\n", proteinID, iAlign);
 	    icnt++;
     	    row = sqlNextRow(sr);
 	    }
     	else
 	    {
 	    fprintf(stderr, "No matching protein found for %s.\n", kgId);
 	    }
 	sqlFreeResult(&sr);
         
 	row3 = sqlNextRow(sr3);
 	}
     sqlFreeResult(&sr3);
     row2 = sqlNextRow(sr2);
     }
 sqlFreeResult(&sr2);
 
 hFreeConn(&conn);
 hFreeConn(&conn2);
 hFreeConn(&conn3);
 fclose(outf);
 return(0);
 }