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/spDbAddVarSplice/spDbAddVarSplice.c src/hg/protein/spDbAddVarSplice/spDbAddVarSplice.c
index 2191cd6..72ab3c8 100644
--- src/hg/protein/spDbAddVarSplice/spDbAddVarSplice.c
+++ src/hg/protein/spDbAddVarSplice/spDbAddVarSplice.c
@@ -1,134 +1,134 @@
 /* spDbAddVarSplice - This adds information on the varient splices to the sp/uniProt 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 "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "portable.h"
 #include "dnautil.h"
 #include "dnaseq.h"
 #include "fa.h"
 #include "jksql.h"
 #include "spDb.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "spDbAddVarSplice - This adds information on the varient splices to the sp/uniProt database\n"
   "usage:\n"
   "   spDbAddVarSplice database varsplice.fasta outDir\n"
   "Where:\n"
   "   database is the database to add to\n"
   "   varSplice.fasta is a fasta file with the splice varients\n"
   "   outDir is where various output tab-generated files live.\n"
   "After this program is done, add the varProtein.txt file into both protein\n"
   "and varProtein tables, add varDisplayId.txt to displayId table, and varAcc.txt\n"
   "into varAcc table, and the varAccToTaxon.txt into the accToTaxon table.\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 FILE *openToWrite(char *dir, char *file)
 /* Return dir/file open for writing. */
 {
 char path[PATH_LEN];
 safef(path, sizeof(path), "%s/%s", dir, file);
 return mustOpen(path, "w");
 }
 
 void spDbAddVarSplice(char *database, char *inFile, char *outDir)
 /* spDbAddVarSplice - This adds information on the varient splices to the sp/uniProt database. */
 {
 struct sqlConnection *conn = sqlConnect(database);
 char query[256];
 makeDir(outDir);
 FILE *varProtein = openToWrite(outDir, "varProtein.txt");
 FILE *varAcc = openToWrite(outDir, "varAcc.txt");
 FILE *varDisplayId = openToWrite(outDir, "varDisplayId.txt");
 FILE *varAccToTaxon = openToWrite(outDir, "varAccToTaxon.txt");
 FILE *varDescription = openToWrite(outDir, "varDescription.txt");
 FILE *varGene = openToWrite(outDir, "varGene.txt");
 FILE *varGeneLogic = openToWrite(outDir, "varGeneLogic.txt");
 struct lineFile *lf = lineFileOpen(inFile, TRUE);
 aaSeq seq;
 ZeroVar(&seq);
 while (faPepSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
     {
     char *row[4];
     char *name = seq.name;
     if (startsWith("sp|", name))	// Skip over sp| introduced Aug 2009
         name += 3;
     int rowSize = chopString(name, "-|", row, ArraySize(row));
     if (rowSize != 3)
         errAbort("Expecting name to be in format accession-N|DISP_ID, got %s\n", name);
     char *acc = row[0];
     char *version = row[1];
     char *displayId = row[2];
     int accLen = strlen(acc);
     int verLen = strlen(version);
     int displayIdLen = strlen(displayId);
 
     /* Do some tests. */
     if ((accLen != 6 && accLen != 10) || isdigit(acc[0]) || !isdigit(acc[accLen-1]))
         errAbort("wierd accession %s before line %d of %s", acc, lf->lineIx, lf->fileName);
     if (!isdigit(version[0]) || verLen > 4)
         errAbort("wierd version %s before line %d of %s", version, lf->lineIx, lf->fileName);
     if (countChars(displayId, '_') != 1 || displayIdLen < 6 || displayIdLen > 16)
         errAbort("wierd displayId %s before line %d of %s", displayId, lf->lineIx, lf->fileName);
     if (accLen + 1 + verLen >= sizeof(SpAcc))
         errAbort("Need to increase size of SpAcc in spDb.h because of %s-%s - need %d characters but only have %lu", acc, version, accLen + 1 + verLen, sizeof(SpAcc));
 
     /* Print out parsed results. */
     fprintf(varAcc, "%s-%s\t%s\t%s\n", acc, version, acc, version);
     fprintf(varProtein, "%s-%s\t%s\n", acc, version, seq.dna);
     fprintf(varDisplayId, "%s-%s\t%s-%s\n", acc, version, acc, version);
 
     /* Look up taxon of base protein and use it to write to varAccToTaxon table. */
     int taxon = spTaxon(conn, acc);
     fprintf(varAccToTaxon, "%s-%s\t%d\n", acc, version, taxon);
 
     /*Transfer description. */
     char *description = spDescription(conn, acc);
     fprintf(varDescription, "%s-%s\t%s\n", acc, version, description);
     freez(&description);
 
     /* Transfer gene logic. */
     sqlSafef(query, sizeof(query), "select val from geneLogic where acc = '%s'", acc);
     char *geneLogic = sqlQuickString(conn, query);
     if (geneLogic != NULL)
         fprintf(varGeneLogic, "%s-%s\t%s\n", acc, version, geneLogic);
     freez(&geneLogic);
 
     /* Transfer genes. */
     struct slName *gene, *geneList = spGenes(conn, acc);
     for (gene = geneList; gene != NULL; gene = gene->next)
         fprintf(varGene, "%s-%s\t%s\n", acc, version, gene->name);
     slFreeList(&geneList);
 
     }
 carefulClose(&varAcc);
 carefulClose(&varProtein);
 carefulClose(&varDisplayId);
 carefulClose(&varAccToTaxon);
 carefulClose(&varDescription);
 carefulClose(&varGene);
 carefulClose(&varGeneLogic);
 sqlDisconnect(&conn);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 4)
     usage();
 spDbAddVarSplice(argv[1], argv[2], argv[3]);
 return 0;
 }