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/spToSpXref2/spToSpXref2.c src/hg/protein/spToSpXref2/spToSpXref2.c
index c0d17c3..6a37fcc 100644
--- src/hg/protein/spToSpXref2/spToSpXref2.c
+++ src/hg/protein/spToSpXref2/spToSpXref2.c
@@ -1,126 +1,126 @@
 /* spToSpXref2- Create tab delimited data file for spXref2 table in proteinsxxxx 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"
 #include "options.h"
 
 #define MAX_EXTDB 500
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "spToSpXref2- Create tab delimited data files for the spXref2 table in uniProt (spxxxxxx) database.\n"
   "usage:\n"
   "   spToSpXref2 swissProt-yymmdd proteome-yymmdd\n"
   "      yymmdd is the release date of SWISS-PROT data\n"
   "Example: spToSpXref2 080707 120323\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn, *conn2;
 char query[256], query2[256];
 struct sqlResult *sr, *sr2;
 char **row, **row2;
 FILE *o1;
 char *proteomeDataDate;
 char *uniprotDataDate;
 char *bioDatabase, *bioentryID;
 char *displayID;
 char *accession;
 char *extAC;
 char *extDb;
 char *division;
 int iii;
 char *extDbName[MAX_EXTDB];
 int icnt;
 int id;
 char *val;
 
 optionHash(&argc, argv);
 if (argc != 3) usage();
 
 uniprotDataDate = argv[1];
 proteomeDataDate = argv[2];
 
 o1 = mustOpen("temp_spXref2.dat", "w");
 
 conn  = hAllocConn(hDefaultDb());
 conn2 = hAllocConn(hDefaultDb());
 
 icnt =0;
 
 /* first read in extDb table */
 sqlSafef(query, sizeof(query), "select * from sp%s.extDb", uniprotDataDate);
 sr = sqlMustGetResult(conn, query);
 row = sqlNextRow(sr);
 while (row != NULL)
     {
     icnt++;
 
     if (icnt >= MAX_EXTDB)
 	{
         errAbort("Too many extDBs - please set MAX_EXTDB to be more than %d\n", MAX_EXTDB);
 	}
     id  = atoi(row[0]);
     val = row[1];
     extDbName[id] = strdup(val);
        
     row = sqlNextRow(sr);
     }
 sqlFreeResult(&sr);
 
 iii=0;
 
 /* Reuse the first 5 fields from the spXref3 table */
 sqlSafef(query2, sizeof(query2), 
       "select accession, displayID, division, bioentryID, biodatabaseID from proteins%s.spXref3;",
       proteomeDataDate);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 iii=0;
 while (row2 != NULL)
     {
     accession		= row2[0];   
     displayID           = row2[1];
     division            = row2[2];
     bioentryID          = row2[3];
     bioDatabase         = row2[4];
   
     sqlSafef(query, sizeof(query),
 	  "select extAcc1, extDb.id from sp%s.extDb, sp%s.extDbRef where extDbRef.acc='%s' %s",
 	  uniprotDataDate, uniprotDataDate, accession, "and extDb.id = extDbRef.extDb;"); 
     sr = sqlMustGetResult(conn, query);
     row = sqlNextRow(sr);
     while (row != NULL)
     	{
     	extAC = row[0];
 	extDb = extDbName[atoi(row[1])];
 
 	printf("%s\t%s\t%s\t%s\t%s\t%s\t%s\n", accession, displayID, division,
 		extDb, extAC, bioentryID, bioDatabase);
  	iii++; 
         
 	if ((iii%100000) == 0)
 	fprintf(stderr, "Processed %d records\n", iii);fflush(stderr);
         
 	row = sqlNextRow(sr);
 	}
     sqlFreeResult(&sr);
     row2 = sqlNextRow(sr2);
     }
 
 fclose(o1);
 
 sqlFreeResult(&sr2);
 hFreeConn(&conn);
 hFreeConn(&conn2);
 
 return(0);
 }