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/kgGetPep/kgGetPep.c src/hg/protein/kgGetPep/kgGetPep.c
index 46e72ba..a6ece66 100644
--- src/hg/protein/kgGetPep/kgGetPep.c
+++ src/hg/protein/kgGetPep/kgGetPep.c
@@ -1,107 +1,107 @@
 /* kgGetPep generates FASTA format protein sequence file to be used for Known Genes track build */
 
 /* 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"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "kgGetPep - generate FASTA format protein sequence file to be used for Known Genes track build.\n"
   "usage:\n"
   "   kgGetPep xxxx\n"
   "            xxxx is the release date of SWISS-PROT database, spxxxx\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn2, *conn3;
 char   query2[256], query3[256];
 struct sqlResult *sr2, *sr3;
 char   **row2, **row3;
 
 char *accession;
 char *displayID;
 char *division;
 char *extDB;
 char *extAC;
     
 char *proteinDataDate;
 
 FILE *o3;
 
 FILE *inf;
 char line[100];
 char *acc;
 char *seq_str;
 char *bioentryID;
 char *databaseID;
 int maxlen = {0};
 int len;
    
 if (argc != 2) usage();
 proteinDataDate = argv[1];
  
 inf = fopen("mrna.lis", "r");
 
 conn2= hAllocConn(hDefaultDb());
 conn3= hAllocConn(hDefaultDb());
     
 o3 = fopen("mrnaPep.tab", "w");
 while (fgets(line, 100, inf) != NULL)
     {
     line[strlen(line)-1] = '\0';
     acc = &line[1];
     
     sqlSafef(query3, sizeof query3,  "select * from proteins%s.spXref2 where extAc='%s' and extDB='EMBL';", 
 	    proteinDataDate, acc);
 
     sr3 = sqlMustGetResult(conn3, query3);
     row3 = sqlNextRow(sr3);
 	      
     while (row3 != NULL)
 	{
    	accession = row3[0];
        	displayID = row3[1];	 
         division  = row3[2];  
 	extDB	  = row3[3];     
 	extAC	  = row3[4];
         bioentryID= row3[5];
 	databaseID= row3[6];
 	
     	sqlSafef(query2, sizeof query2, "select val from sp%s.protein where acc='%s';", 
 		proteinDataDate, accession);
     	
 	sr2 = sqlMustGetResult(conn2, query2);
     	row2 = sqlNextRow(sr2);
     	while (row2 != NULL)
 	    {
  	    seq_str = row2[0];
 	    	
 	    len = strlen(seq_str);
 	    if (maxlen < len) maxlen = len;
 		
 	    printf(">%s\n%s\n", acc, seq_str);
 	    fprintf(o3, "%s\t%s\n", acc, seq_str);
 		
 	    row2 = sqlNextRow(sr2);
 	    }
 		
         sqlFreeResult(&sr2);
 	row3 = sqlNextRow(sr3);
 	}
     sqlFreeResult(&sr3);
     }
     
 //fprintf(stderr, "Max AA length = %d\n", maxlen);
 
 hFreeConn(&conn2);
 hFreeConn(&conn3);
 	
 fclose(o3);
 return(0);
 }