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/makeDb/outside/hgSuperfam/hgSuperfam.c src/hg/makeDb/outside/hgSuperfam/hgSuperfam.c
index 16c36eb..486f2e1 100644
--- src/hg/makeDb/outside/hgSuperfam/hgSuperfam.c
+++ src/hg/makeDb/outside/hgSuperfam/hgSuperfam.c
@@ -1,147 +1,147 @@
 /* hgSuperfam - make tables for Supfamily track */
 
 /* 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"
 
 #define MAX_LOG_EVALUE 730.0
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgSuperfam - Generate supfamily table for the Superfamily track.\n"
   "usage:\n"
   "   hgSuperfam gDb pDb\n"
   "      gDb   is the genome database\n"
   "      sDb   is the superfamily database\n"
   "example: hgSuperfam mm5 superfam041128\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn, *connEnsGene, *connSf;
 char query[256], query2[256];
 struct sqlResult *sr, *sr2;
 char **row, **row2;
 char cond_str[200];
 
 char *seqID, *eValue, *sfID, *sfDesc;
 char *name, *chrom, *cdsStart, *cdsEnd;
 float E,score;
 
 char *translation_name = NULL;
 
 char *genomeDb, *superfamDb;
 char gene_name[200];
 
 char *chp;
 
 FILE *o3, *o4;
    
 if (argc != 3) usage();
 genomeDb = argv[1];
 superfamDb = argv[2];
  
 o3 = mustOpen("j.dat", "w");
 o4 = mustOpen("jj.dat", "w");
 
 conn = hAllocConn(genomeDb);
 connEnsGene= hAllocConn(genomeDb);
 connSf= hAllocConn(genomeDb);
 
 sqlSafef(query2,sizeof(query2),"select * from %s.ensGene;", genomeDb);
 
 sr2 = sqlMustGetResult(connEnsGene, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     name 	= row2[0];
     chrom 	= row2[1];
     cdsStart	= row2[5]; 
     cdsEnd	= row2[6];
 			
     strcpy(gene_name, name);
 
     
     /* get rid of version number */
     chp = strstr(name, ".");
     if (chp != NULL) *chp = '\0';
 
     if (hTableExists(genomeDb, "ensGeneXref"))
         {
         sqlSafefFrag(cond_str, sizeof(cond_str), "transcript_name='%s'", name);
         translation_name = sqlGetField(genomeDb, "ensGeneXref", "translation_name", cond_str);
         }
     if (hTableExists(genomeDb,"ensemblXref3") && translation_name == NULL)
         {
         sqlSafefFrag(cond_str, sizeof(cond_str), "transcript='%s'", name);
         translation_name = sqlGetField(genomeDb, "ensemblXref3", "protein", cond_str);
         }
     if (translation_name == NULL) 
 	{
 	printf("transcript not found, skipping %s\n", name);
 	fflush(stdout);
 	}
     else
 	{
 	/* get rid of version number */
     	chp = strstr(translation_name, ".");
     	if (chp != NULL) *chp = '\0';
 
     	sqlSafef(query, sizeof query, "select * from %s.sfAssign where seqID='%s'", superfamDb, translation_name);
     	sr = sqlMustGetResult(conn, query);
     	row = sqlNextRow(sr);
 
     	if (row == NULL) 
 	    {
 	    printf("%s not found in sfAssign!\n", translation_name);
 	    fflush(stdout);
 	    }
 
     	while (row != NULL)
             {      
  	    seqID 	= row[1];
  	    eValue	= row[4];
  	    sfID	= row[5];
  	    sfDesc	= row[6];	/* 0302 and other supfam releases has an error here */
 		
 	    sqlSafefFrag(cond_str, sizeof cond_str, "id=%s", sfID);
 	    sfDesc  = sqlGetField(superfamDb, "des", "description", cond_str);
 
 	    E = atof(eValue);
 	    if (E > 0.02) continue;
 
 	    score = (-log(E)/MAX_LOG_EVALUE)*10000.0;
 	    if (score <= 0.0) score = 0.0;
 	    if (score > 1000.0) score = 1000.0;
 		
 	    fprintf(o3, "%s\t%s\t%s\t%s\n", chrom, cdsStart, cdsEnd, name);
 	    fprintf(o4, "%s\t%s\t%s\n", name, seqID, sfDesc);
             row = sqlNextRow(sr);
 	    }
     	sqlFreeResult(&sr);
     	}
     row2 = sqlNextRow(sr2);
     }
 
 sqlFreeResult(&sr2);
 
 hFreeConn(&conn);
 hFreeConn(&connEnsGene);
 hFreeConn(&connSf);
     
 fclose(o3);
 fclose(o4);
 
 mustSystem("cat j.dat |sort|uniq  > superfamily.tab");
 mustSystem("cat jj.dat|sort|uniq  > sfDescription.tab");
 mustSystem("rm j.dat");
 mustSystem("rm jj.dat");
    
 return(0);
 }