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/oneShot/kgName/kgName.c src/hg/oneShot/kgName/kgName.c
index 7df0266..e53f934 100644
--- src/hg/oneShot/kgName/kgName.c
+++ src/hg/oneShot/kgName/kgName.c
@@ -1,164 +1,164 @@
 /* kgName - builds association table between knownPep and gene common name. */
 
 /* 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 "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "hCommon.h"
 #include "hdb.h"
 #include "spDb.h"
 
 char *database = "hg16";
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "kgName - builds association table between knownPep and gene common name\n"
   "usage:\n"
   "   kgName database reference.psl outAssoc \n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 char *protDbName = NULL;
 
 char* lookupName(  struct sqlConnection *conn , char *id)
 {
 char query[256];
 char *name = id;
 
 if (hTableExists("kgXref"))
     {
     struct sqlResult *sr;
     char **row;
 
     sqlSafef(query, sizeof query, "select geneSymbol from kgXref where mRNA = '%s'", id);
     sr = sqlGetResult(conn, query);
     row = sqlNextRow(sr);
     if (row != NULL)
 	{
 	name = cloneString(row[0]);
 	}
     sqlFreeResult(&sr);
     }
 #ifdef NOTNOW
 if (hTableExists("refLink") && hTableExists("knownGeneLink"))
     {
     struct sqlResult *sr;
     char **row;
 
     sqlSafefFrag(cond_str, sizeof cond_str, "name='%s' and seqType='g'", id);
     seqType = sqlGetField(conn, database, "knownGeneLink", "seqType", cond_str);
 
     if (seqType != NULL)
 	{
 	// special processing for RefSeq DNA based genes
 	qlSafefFrag(cond_str, sizeof cond_str, "mrnaAcc = '%s'", id);
 	refSeqName = sqlGetField(conn, database, "refLink", "name", cond_str);
 	if (refSeqName != NULL)
 	    {
 	    name=  cloneString(refSeqName);
 	    }
 	}
     else if (protDbName != NULL)
 	{
 	sqlSafefFrag(cond_str, sizeof cond_str, "mrnaID='%s'", id);
 	proteinID = sqlGetField(conn, database, "spMrna", "spID", cond_str);
 
 	sqlSafefFrag(cond_str, sizeof cond_str, "displayID = '%s'", proteinID);
 	hugoID = sqlGetField(conn, protDbName, "spXref3", "hugoSymbol", cond_str);
 	if (!((hugoID == NULL) || (*hugoID == '\0')) )
 	    {
 	    name= cloneString(hugoID);
 	    }
 	else
 	    {
 	    sqlSafef(query, sizeof query,"select refseq from %s.mrnaRefseq where mrna = '%s';",  
 		    database, id);
 
 	    sr = sqlGetResult(conn, query);
 	    row = sqlNextRow(sr);
 	    if (row != NULL)
 		{
 		sqlSafef(query, sizeof query, "select * from refLink where mrnaAcc = '%s'", row[0]);
 		sqlFreeResult(&sr);
 		sr = sqlGetResult(conn, query); 
 		if ((row = sqlNextRow(sr)) != NULL)
 		    {
 		    if (strlen(row[0]) > 0)
 			name= cloneString(row[0]);
 		    }
 		sqlFreeResult(&sr);
 		}
 	    else
 		{
 		sqlFreeResult(&sr);
 		}
 	    }
 	}
     }
 #endif
 return name;
 }
 
 char *getSwiss( struct sqlConnection *conn , char *id)
 {
 char query[256];
 char *name = NULL;
 if (hTableExists("kgXref"))
     {
     struct sqlResult *sr;
     char **row;
 
     sqlSafef(query, sizeof query, "select spID from kgXref where mRNA = '%s'", id);
     sr = sqlGetResult(conn, query);
     row = sqlNextRow(sr);
     if (row != NULL)
 	{
 	name = cloneString(row[0]);
 	sqlFreeResult(&sr);
 	return name;
 	}
 	sqlFreeResult(&sr);
     }
 errAbort("no kgXref");
 }
 
 void kgName(char *database, char *protDb, char *refPsl,  char *outAssoc)
 /* kgName - builds association table between knownPep and gene common name. */
 {
 struct sqlConnection *conn = sqlConnect(database);
 //struct sqlConnection *conn2 = sqlConnect("uniProt");
 FILE *f = mustOpen(outAssoc, "w");
 struct lineFile *pslLf = pslFileOpen(refPsl);
 struct psl *psl;
 
 while ((psl = pslNext(pslLf)) != NULL)
     fprintf(f,"%s\t%s\t%s:%d-%d\t%s\n",psl->qName, lookupName(conn,psl->qName), 
 	psl->tName, psl->tStart, psl->tEnd, getSwiss(conn, psl->qName));
 /*
 while (lineFileRow(lf, words))
     {
     fprintf(f,"%s\t%s\t%s\n",words[0], lookupName(conn,words[0]), getSwiss(conn, words[0]));
     }
     */
 //hFreeConn(&conn);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 4)
     usage();
 database=argv[1];
 hSetDb(argv[1]);
 protDbName = hPdbFromGdb(database);
 kgName(argv[1], protDbName, argv[2], argv[3]);
 return 0;
 }