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/getInterProFa/getInterProFa.c src/hg/protein/getInterProFa/getInterProFa.c
index c4817a0..a8116d0 100644
--- src/hg/protein/getInterProFa/getInterProFa.c
+++ src/hg/protein/getInterProFa/getInterProFa.c
@@ -1,121 +1,121 @@
 /* getInterProFa - get AA sequence of InterPro domains for a specific organism */
 
 /* 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(
   "getInterProFa - get AA sequence of InterPro domains for a specific organism\n"
   "usage:\n"
   "   getInterProFa tableName outFileName\n"
   "      tableName is the InterPro xref table name for the specific organism\n"
   "      outFileName is the output file name\n"
   "example: getInterProFa interProXrefHiv1 interProHiv1.fa\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn2, *conn3, *conn4;
 char query2[256], query3[256], query4[256];
 struct sqlResult *sr2, *sr3, *sr4;
 char **row2, **row3, **row4;
 
 char *aaSeq;
 char *accession;
 char *desc;
 
 FILE *outFile;
 char *outFileName;
 char *tableName;
 
 char *interProId;
 int  maxLen, len;
 char *maxAcc = NULL;
 char *start, *end;
 char *maxStart=NULL, *maxEnd=NULL, *maxDesc = NULL;
 
 if (argc != 3) usage();
 tableName    = argv[1];
 outFileName  = argv[2];
    
 outFile = mustOpen(outFileName, "w");
 conn2 = hAllocConn();
 conn3 = hAllocConn();
 conn4 = hAllocConn();
 	
 /* loop over all InterPro entry for the specific InterPro xref table for this organism */
 sqlSafef(query2, sizeof query2, "select distinct interProId from proteome.%s", tableName);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     interProId  = row2[0];
     
     /* get all start/end positions of this InterPro domain */ 
     sqlSafef(query3, sizeof query3,
     "select accession, start, end, description from proteome.%s where interProId='%s'", 
     tableName, interProId);
     sr3 = sqlMustGetResult(conn3, query3);
     row3 = sqlNextRow(sr3);
 
     maxLen = 0;
     while (row3 != NULL)
 	{
    	accession = row3[0];
        	start     = row3[1];	 
         end       = row3[2];  
 	desc      = row3[3];
 	len = atoi(end) - atoi(start) + 1;
 	
 	/* remember the max len, so far */
 	if (len > maxLen)
 	    {
 	    maxLen   = len;
 	    maxAcc   = cloneString(accession);
 	    maxStart = cloneString(start);
 	    maxEnd   = cloneString(end);
 	    maxDesc  = cloneString(desc);
 	    }
 	    
 	row3 = sqlNextRow(sr3);
 	}
     sqlFreeResult(&sr3);
     
     /* fetch the corresponding AA sequence of the domain having the max length */
     sqlSafef(query4, sizeof query4, "select substring(val, %s, %d) from uniProt.protein where acc='%s'",
     	    maxStart, maxLen, maxAcc);
     sr4 = sqlMustGetResult(conn4, query4);
     row4 = sqlNextRow(sr4);
     if (row4 == NULL)
     	{
 	fprintf(stderr, "%s %s missing, exiting ...\n", maxAcc, interProId);
 	exit(1);
 	}
     else
     	{
 	aaSeq = row4[0];
 	if (maxLen >= 18)
 	    {
 	    fprintf(outFile, ">%s %s\n", interProId, maxDesc);
 	    fprintf(outFile, "%s\n", aaSeq);fflush(stdout);
 	    }
 	}
     sqlFreeResult(&sr4);	   
     
     row2 = sqlNextRow(sr2);
     }
 sqlFreeResult(&sr2);
 
 hFreeConn(&conn2);
 hFreeConn(&conn3);
 hFreeConn(&conn4);
 
 fclose(outFile);
 return(0);
 }