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/kgSelect/kgSelect.c src/hg/protein/kgSelect/kgSelect.c
index cf4e27a..44e98a2 100644
--- src/hg/protein/kgSelect/kgSelect.c
+++ src/hg/protein/kgSelect/kgSelect.c
@@ -1,112 +1,112 @@
 /* kgSelect - select the highest scoring mrna (or RefSeq) from the protMrnaScore 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(
   "kgSelect - select the highest scoring mrna (or RefSeq) from the protMrnaScore table\n"
   "usage:\n"
   "   kgSelect tempDb outfile\n"
   "      tempDb is the temp DB name\n"
   "      outfile is the output file name\n"
   "example: kgSelect kgMm6ATemp kgTemp2.gp\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn2, *conn3, *conn4;
 char query2[256], query3[256], query4[256];
 struct sqlResult *sr2, *sr3, *sr4;
 char **row2, **row3, **row4;
 char *kgTempDb;
 char *outfileName;
 FILE *outf;
 int  alignCnt = 0;
 char *score;
 int  i;
 char protMrnaName[255];
 char *chp;
 char *protAcc, *mrnaAcc;
 char srcType;
 char *geneName;
 
 if (argc != 3) usage();
 kgTempDb    = argv[1];
 outfileName = argv[2];
 
 outf = mustOpen(outfileName, "w");
 conn2= hAllocConn();
 conn3= hAllocConn();
 conn4= hAllocConn();
 
 /* go through each protein */
 sqlSafef(query2, sizeof(query2), "select distinct protAcc from %s.protMrnaScore", kgTempDb);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     /* get all prot/mRna pairs in score table with this protein, ordered by score */
     protAcc = row2[0];
     sqlSafef(query3, sizeof(query3), 
             "select mrnaAcc, score from %s.protMrnaScore where protAcc='%s' order by score desc limit 1", 
     	    kgTempDb, protAcc);
     sr3  = sqlMustGetResult(conn3, query3);
     row3 = sqlNextRow(sr3);
 	      
     /* get the top scoring mRNA or RefSeq */	      
     if (row3 != NULL)
 	{
    	mrnaAcc = row3[0];
 	score   = row3[1];
 	safef(protMrnaName, sizeof(protMrnaName), "%s_%s", protAcc, mrnaAcc);
 	sqlSafef(query4, sizeof(query4), 
 		"select * from %s.kgCandidate where name='%s' or name='%s'", 
 		kgTempDb, mrnaAcc, protMrnaName);
     	sr4  = sqlMustGetResult(conn4, query4);
     	row4 = sqlNextRow(sr4);
 	if (row4 != NULL)
 	    {
 	    geneName = strdup(row4[0]);
 	    chp = strstr(geneName, "_");
 	    if (chp != NULL)
 	    	{
 		if (strstr(geneName, "NM_") != NULL)
 		    {
 		    srcType = 'R';	/* src is RefSeq */
 		    }
 		else
 		    {
 		    chp++;
 		    geneName = chp;
 		    srcType  = 'U';	/* src is UCSC prot/mrna alignment */
 		    }
 		}
 	    else
 	    	{
 		srcType = 'G';		/* src is GenBank */
 		}
 	    alignCnt++;
 	    fprintf(outf, "%s\t", geneName);
 	    for (i= 1; i<10; i++) fprintf(outf, "%s\t", row4[i]);
 	    fprintf(outf, "%s\t%c_%d\n", protAcc, srcType, alignCnt);fflush(stdout);
 	    }
         sqlFreeResult(&sr4);
         row3 = sqlNextRow(sr3);
 	}
     sqlFreeResult(&sr3);
     row2 = sqlNextRow(sr2);
     }
 sqlFreeResult(&sr2);
 
 hFreeConn(&conn2);
 hFreeConn(&conn3);
 fclose(outf);
 return(0);
 }