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/oneShot/makeOrthoAtgTable/makeOrthoAtgTable.c src/hg/oneShot/makeOrthoAtgTable/makeOrthoAtgTable.c
index c3fec3c..f5da88e 100644
--- src/hg/oneShot/makeOrthoAtgTable/makeOrthoAtgTable.c
+++ src/hg/oneShot/makeOrthoAtgTable/makeOrthoAtgTable.c
@@ -1,124 +1,124 @@
 /* makeOrthoAtgTable - Create a table that lists how often atg, kozak, stop is conserved based on output from txCdsOrtho.. */
 
 /* 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 "jksql.h"
 #include "hdb.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "makeOrthoAtgTable - Create a table that lists how often atg, kozak, stop is conserved based on output from txCdsOrtho.\n"
   "usage:\n"
   "   makeOrthoAtgTable totalOrfs species1.tab species2.tab ...\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 void analyzeOne(int totalOrfs, char *fileName)
 /* Do analysis on one tab-separated file. */
 {
 int nativeAtgCount = 0, nativeKozakCount = 0, nativeStopCount = 0;
 int atgCount = 0, kozakCount = 0, stopCount=0, count = 0;
 int atgAli = 0, kozakAli = 0, stopAli = 0;
 double totalOrfSizeRatio = 0.0;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[18];
 while (lineFileRow(lf, row))
     {
     boolean xenoAtg = (row[10][0] == '1');
     boolean xenoKozak = (row[11][0] == '1');
     boolean xenoStop = (row[12][0] == '1');
     boolean nativeAtg = (row[13][0] == '1');
     boolean nativeKozak = (row[14][0] == '1');
     boolean nativeStop = (row[15][0] == '1');
     int atgDotCount = lineFileNeedNum(lf, row, 4);
     int kozakDotCount = lineFileNeedNum(lf, row, 6);
     int stopDotCount = lineFileNeedNum(lf, row, 8);
     int possibleOrfSize = lineFileNeedNum(lf, row, 16);
     int orfSize = lineFileNeedNum(lf, row, 17);
     double orfSizeRatio = (double)orfSize/possibleOrfSize;
     totalOrfSizeRatio += orfSizeRatio;
     if (nativeAtg)
        {
        ++nativeAtgCount;
        if (atgDotCount == 0)
 	   {
 	   ++atgAli;
 	   if (xenoAtg)
 	       ++atgCount;
 	   }
        }
     if (nativeKozak)
        {
        ++nativeKozakCount;
        if (kozakDotCount == 0 && atgDotCount == 0)
 	   {
 	   ++kozakAli;
 	   if (xenoKozak)
 	       ++kozakCount;
 	   }
        }
     if (nativeStop)
        {
        ++nativeStopCount;
        if (stopDotCount == 0)
 	   {
 	   ++stopAli;
 	   if (xenoStop)
 	       ++stopCount;
 	   }
        }
     ++count;
     }
 char dbName[256];
 splitPath(fileName, NULL, dbName, NULL);
 
 struct sqlConnection *conn = hConnectCentral();
 char query[512];
 sqlSafef(query, sizeof(query), "select organism from dbDb where name='%s'", dbName);
 char *organism = sqlQuickString(conn, query);
 sqlSafef(query, sizeof(query), "select scientificName from dbDb where name='%s'", dbName);
 char *scientificName = sqlQuickString(conn, query);
 hDisconnectCentral(&conn);
 
 printf("%s\t%s\t%s\t", organism, scientificName, dbName);
 printf("%4.2f%%\t", 100.0 * count/totalOrfs);
 printf("%4.2f%%\t", 100.0 * atgAli/nativeAtgCount);
 printf("%4.2f%%\t", 100.0 * atgCount/atgAli);
 // printf("%4.2f%%\t", 100.0 * kozakAli/nativeKozakCount);
 // printf("%4.2f%%\t", 100.0 * kozakCount/kozakAli);
 printf("%4.2f%%\t", 100.0 * stopAli/nativeStopCount);
 printf("%4.2f%%\t", 100.0 * stopCount/stopAli);
 printf("%4.2f%%\n", 100.0 * totalOrfSizeRatio/count);
 }
 
 void makeOrthoAtgTable(int totalOrfs, int fileCount, char *files[])
 /* makeOrthoAtgTable - Create a table that lists how often atg, kozak, stop is conserved based on output from txCdsOrtho.. */
 {
 int i;
 printf("species\tbinomial name\tdb\t%%genes\t%%startAli\t%%startId\t%%stopAli\t%%stopId\t%%orfCover\n");
 for (i=0; i<fileCount; ++i)
     analyzeOne(totalOrfs, files[i]);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc < 3)
     usage();
 makeOrthoAtgTable(atoi(argv[1]), argc-2, argv+2);
 return 0;
 }