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/spToProteinsVar/spToProteinsVar.c src/hg/protein/spToProteinsVar/spToProteinsVar.c
index 833386f..13f91fc 100644
--- src/hg/protein/spToProteinsVar/spToProteinsVar.c
+++ src/hg/protein/spToProteinsVar/spToProteinsVar.c
@@ -1,89 +1,89 @@
 /* spToProteinsVar- Create tab delimited data file, spXref3Var.tab, for variant splice proteins in proteinsYYMMDD database */
 
 /* 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"
 #include "spDb.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "spToProteinsVar- Create tab delimited data file, spXrefVar.tab,\n"
   "from spYYMMDD database for proteinsYYMMDD database.\n"
   "usage:\n"
   "   spToProteinsVar YYMMDD\n"
   "      YYMMDD is the release date of SWISS-PROT data\n"
   "Example: spToProteinsVar 050415\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn, *conn2;
 char query2[256];
 struct sqlResult *sr2;
 char **row2;
 char cond_str[255];
 char proteinDatabaseName[255];
 char proteinsDB[255];
 char *bioDatabase;
 char *desc;
 char *hugoSymbol, *hugoDesc;
 FILE *o2;
 char *proteinDataDate;
 int  bioentryId;
 char *displayId;
 char *acc;
 char *parAcc;
 char *division;
 
 if (argc != 2) usage();
 
 proteinDataDate = argv[1];
 sprintf(proteinDatabaseName, "sp%s", proteinDataDate);
 sprintf(proteinsDB, "proteins%s", proteinDataDate);
 
 o2 = mustOpen("spXref3Var.tab", "w");
 
 conn  = hAllocConn(hDefaultDb());
 conn2 = hAllocConn(hDefaultDb());
 
 bioentryId = 9000000;	/* to differentiate with regular proteins */
 
 sqlSafef(query2, sizeof query2, "select * from %s.varProtTemp;", proteinDatabaseName);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     bioentryId++;
     acc		= row2[0];   
     bioDatabase = row2[1];
     parAcc      = row2[2];
     desc        = row2[3];
     
     /* set display ID the same as accession for variant splice proteins */
     displayId = acc;
     
     /* duplicate the following info from its parent protein */
     sqlSafefFrag(cond_str, sizeof cond_str, "accession='%s'", parAcc);
     division   = sqlGetField(proteinsDB, "spXref3", "division", cond_str);
     hugoSymbol = sqlGetField(proteinsDB, "spXref3", "hugoSymbol", cond_str);
     hugoDesc   = sqlGetField(proteinsDB, "spXref3", "hugoDesc", cond_str);
     
     fprintf(o2, "%s\t%s\t%s\t%d\t%s\t%s\t%s\t%s\n", acc, displayId, 
 	    division, bioentryId, bioDatabase, desc, hugoSymbol, hugoDesc);
     
    row2 = sqlNextRow(sr2);
    }
 
 fclose(o2);
 
 sqlFreeResult(&sr2);
 hFreeConn(&conn);
 hFreeConn(&conn2);
 
 return(0);
 }