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/near/knownToHprd/knownToHprd.c src/hg/near/knownToHprd/knownToHprd.c
index 0974499..5d2c87a 100644
--- src/hg/near/knownToHprd/knownToHprd.c
+++ src/hg/near/knownToHprd/knownToHprd.c
@@ -1,138 +1,138 @@
 /* knownToHprd - Create knownToHprd table by reading HPRD FLAT_FILES and using kgXref.
  *   This utilility should make automating incremental kg build easier. 
  *   It is assumed that the HPRD flat files have been decompressed in
  *   a directory like /cluster/data/hg18/p2p/hprd/FLAT_FILES/ 
  *   The data has this structure:
 [hgwdev:FLAT_FILES> head HPRD_ID_MAPPINGS.txt
 00001   ALDH1A1 NM_000689.3     NP_000680.2     216     100640  P00352  Aldehyde dehydrogenase 1
  */
 
 /* 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 "dystring.h"
 #include "options.h"
 #include "jksql.h"
 #include "hdb.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "knownToHprd - Create knownToHprd table using HPRD flat file and kgXref\n"
   "usage:\n"
   "   knownToHprd database hprdFile\n"
   "options:\n"
   "   -keepTab - temp tab file not removed during cleanup.\n"
   );
 }
 
 char *outTable = "knownToHprd";
 
 static struct optionSpec options[] = {
    {"keepTab", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 void createTable(struct sqlConnection *conn, char *tableName)
 /* Create our name/value table, dropping if it already exists. */
 {
 struct dyString *dy = dyStringNew(512);
 sqlDyStringPrintf(dy,
 "CREATE TABLE  %s (\n"
 "    name varchar(255) not null,\n"
 "    value varchar(255) not null,\n"
 "#Indices\n"
 "    PRIMARY KEY(name),\n"
 "    INDEX(value)\n"
 ")\n",  tableName);
 sqlRemakeTable(conn, tableName, dy->string);
 dyStringFree(&dy);
 }
 
 
 void knownToHprd(char *database, char *hprdFile)
 /* knownToHprd - Create knownToHprd table by using hprd flat file and kgXref. */
 {
 char *tempDir = ".";
 FILE *f = hgCreateTabFile(tempDir, outTable);
 struct lineFile *lf = lineFileOpen(hprdFile, TRUE);
 char *lrow[8];
 
 struct sqlConnection *hConn = sqlConnect(database);
 struct sqlResult *sr;
 char **row;
 struct hash *mRnaHash = newHash(18);
 struct hash *spIdHash = newHash(18);
 struct hash *kgIdHash = newHash(18);
 int missing=0;  // how many recs had no match via kgXref
 
 sr = sqlGetResult(hConn, NOSQLINJ "select kgId, mRNA, spId from kgXref");
 while ((row = sqlNextRow(sr)) != NULL)
     {
     char *kgId = row[0];
     char *mRNA = row[1];
     char *spId = row[2];
     hashAdd(mRnaHash, mRNA, cloneString(kgId));
     if (spId && spId[0])
 	hashAdd(spIdHash, spId, cloneString(kgId));
     }
 sqlFreeResult(&sr);
 
 while (lineFileRowTab(lf, lrow))
     {
     char *hprdId = lrow[0];
     char *cDna = lrow[2];
     char *uniProt = lrow[6];
     struct hashEl *kgId = NULL;
     chopSuffixAt(cDna,'.');
 
     boolean found = FALSE;
     for (kgId = hashLookup(mRnaHash, cDna); kgId; kgId = hashLookupNext(kgId))
 	{
 	found = TRUE;
 	if (!hashLookup(kgIdHash, kgId->val))  // each kgId only once 
 	    {
 	    hashAdd(kgIdHash, kgId->val, NULL);
 	    fprintf(f,"%s\t%s\n",(char *)kgId->val,hprdId);
 	    }
 	}
 
     for (kgId = hashLookup(spIdHash, uniProt); kgId; kgId = hashLookupNext(kgId))
 	{
 	found = TRUE;
 	if (!hashLookup(kgIdHash, kgId->val))  // each kgId only once 
 	    {
 	    hashAdd(kgIdHash, kgId->val, NULL);
 	    fprintf(f,"%s\t%s\n",(char *)kgId->val,hprdId);
 	    }
 	}
 
     if (!found)
 	{
 	++missing;
 	verbose(2, "missing %s %s %s\n", hprdId, cDna, uniProt);
 	}
     }
 lineFileClose(&lf);
 carefulClose(&f);
 
 verbose(2, "missing=%d\n",missing);
 
 createTable(hConn, outTable);
 hgLoadTabFile(hConn, tempDir, outTable, &f);
 if (!optionExists("keepTab"))
     hgRemoveTabFile(tempDir, outTable);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 knownToHprd(argv[1],argv[2]);
 return 0;
 }