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Re: Counter help

#11

Mar 27th, 2008

Oh, and I tried the above suggestion, but that didn't work either. Still weird numbers.

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Re: Counter help

#12

Mar 27th, 2008

> ... but that didn't work either. Still weird numbers.

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  assert( ( matrix[i][3] == 0  ) || ( matrix[i][3] == 1 ) ) ; 
  assert( ( matrix[i][4] == 0 ) || ( matrix[i][4] == 1 ) ) ; 
  int sum =  matrix[i][3] + matrix[i][4] ;
  if( sum == 2 ) ++counters[1][1] ;
  else if( sum == 1 ) ++counters[0][1] ;
  else ++counters[0][0] ;

Last edited by vijayan121; Mar 27th, 2008 at 3:27 pm.

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Re: Counter help

#13

Mar 27th, 2008

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Originally Posted by andyg55

Hate to do this vernon but...

counters array???

I think I cut and pasted your first post before I saw your second. You had:

 Help with Code Tags 
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int counters[2][2] = {0};
int counters[2][2] = {0};

declared at the top, but I never saw it used later in the code. Looks like post 2 has it.

Last edited by VernonDozier; Mar 27th, 2008 at 3:28 pm.

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Re: Counter help

#14

Mar 27th, 2008

The code you posted previously for doing the counting:

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      for(i = 0; i < 10; i++)          // Set the counter for the genotypes
      {
         if (matrix[i][3]==0  && matrix[i][4] ==0)   // If alleles AA, increase counter [0][0] by 1
         { 
            counters[0][0]++; 
         }
 
         else
            if (matrix[i][3]==0  && matrix[i][4] ==1 || matrix[i][3]==1  && matrix[i][4] ==0) // If allele is heterozygous, increase counter [0][1] by 1
            { 
               counters[0][1]++; 
            }
 
            else
               if (matrix[i][3]==1 && matrix[i][4] ==1)    // If alleles BB, increase counter [1][1] by 1
               {
                  counters[1][1]++;
               }
      }
      for(i = 0; i < 10; i++)          // Set the counter for the genotypes
      {
         if (matrix[i][3]==0  && matrix[i][4] ==0)   // If alleles AA, increase counter [0][0] by 1
         { 
            counters[0][0]++; 
         }

         else
            if (matrix[i][3]==0  && matrix[i][4] ==1 || matrix[i][3]==1  && matrix[i][4] ==0) // If allele is heterozygous, increase counter [0][1] by 1
            { 
               counters[0][1]++; 
            }

            else
               if (matrix[i][3]==1 && matrix[i][4] ==1)    // If alleles BB, increase counter [1][1] by 1
               {
                  counters[1][1]++;
               }
      }

Seems OK. I don't see why the 0-0 combination is not being counted, and the cumulative counts don't correctly increment, seems they just keep adding the original value, in this example.

Have you changed this part?

Last edited by vmanes; Mar 27th, 2008 at 3:30 pm.

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Re: Counter help

#15

Mar 27th, 2008

That asseret didnt work either... just doubles 10 and 11, leaving 00 as zero.

Yeah the counters are there... they're just not working

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Re: Counter help

#16

Mar 27th, 2008

yeah i tried changing that part to different combinations of code that mean the same thing... no change though

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Re: Counter help

#17

Mar 27th, 2008

Please show your current version. And a set of results that it generates.

Last edited by vmanes; Mar 27th, 2008 at 3:36 pm.

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Re: Counter help

#18

Mar 27th, 2008

 Help with Code Tags 
 C++ Syntax (Toggle Plain Text) 
#include <fstream.h>
#include <stdlib.h>
#include <assert.h>
 
 
int i, j;
int matrix[10000][5] = {0};                              //Define a matrix with a maximum of 100 rows and 6 columns
int counters[2][2] = {0};                                // Define the genotype counter     
int repeats = 0;
int norepeats;
float p, q;
float rand1, rand2, rand3, rand4;
void SetSeed();
 
int main () {
 
FILE *output_file = fopen("output.txt", "w");
 
printf("Enter the frequency of allele A: ");
scanf("%f", &p);
printf("\n");
printf("Frequency of allele A (p) is: %.3f\n", p);       // States the frequency of the A allele
q = 1 - p;                                               // The value of q is 1 - (the probability entered for p)
 
printf("Frequency of allele B (q) is: %.3f\n", q);       // States the frequency of the B allele
printf("\n");
printf("Please enter the desired number of repeats: ");
scanf("%d", &norepeats);                                 // Desired number of repeats of the program stored in 'norepeats'
printf("\n");
 
while (repeats != norepeats){                            // A while loop to loop the program 'norepeats' amount of times
 
const float RANGE = 1.0;                                 // Random number generated is below 1
SetSeed();                                               // Seed file for RNG set here
 
//Open the input file//
ifstream inFile;
inFile.open("input.txt");                                // Genealogy input file opened
 
  if (!inFile)
  {
  printf ("Unable to open input file");                  // Error message reported if input.txt cannot be opened
  exit(1);
  }
 
//Read the input file into the array
while (inFile >> matrix[i][0])
{
printf ("%d\t", matrix[i][0]);
for (j = 1; j < 3; j++)
{
inFile >> matrix[i][j];
printf ("%d\t", matrix[i][j]);
}
 
int counter;
 
if (matrix[i][1] == 0 && matrix[i][2] == 0){             // If the individual is a founder:
 
   rand1 = (float) rand() * RANGE / RAND_MAX;            // Random number 1 generated 
   rand2 = (float) rand() * RANGE / RAND_MAX;            // Random number 2 generated
 
   if (rand1 < p){                                       // Place a 0 allele down in column 4 if random number 1 is below the set p value
   matrix[i][3] = 0;
   }   
   else{
   matrix[i][3] = 1;                                     // Place a 1 allele down in column 4 if random number 1 is above the set p value
   }      
   printf("\t%d", matrix[i][3]);
 
 
   if (rand2 < p){                                       // Place a 0 allele down in column 5 if random number 2 is below the set p value
   matrix[i][4] = 0;
   }      
   else{                                                 // Place a 1 allele down in column 5 if random number 2 is above the set p value
   matrix[i][4] = 1;
   }
   printf("\t%d", matrix[i][4]);
   }
 
else{
   int dad = matrix[i][1];                               // 1 is "dad" column
   int mum = matrix[i][2];                               // 2 is "mum" column
 
   int dadRowIndex = dad - 1;                            // The row of the father is 'dad - 1' as the first row is set at zero
   int mumRowIndex = mum -1;                             // The row of the mother is 'mum - 1' as the first row is set at zero
 
   for (counter = 1;counter <= 1;counter++){
   rand3 = (float) rand() * RANGE / RAND_MAX;            // Random number 3 generated
   rand4 = (float) rand() * RANGE / RAND_MAX;            // Random number 4 generated
   }
   if (rand3 < 0.5){                                     // If random number 3 is less than a half, receive allele stored in column 4 from dad
   matrix[i][3] = matrix[dadRowIndex][3];
   }   
   else{                                                 // If random number 3 is more than a half, receive allele stored in column 5 from dad
   matrix[i][3] = matrix[dadRowIndex][4];
   }
   printf("\t%d", matrix[i][3]);
 
   if (rand4 < 0.5){                                     // If random number 4 is less than a half, receive allele stored in column 4 from mum
   matrix[i][4] = matrix[mumRowIndex][3];
   }
   else{                                                 // If random number 4 is more than a half, receive allele stored in column 5 from mum
   matrix[i][4] = matrix[mumRowIndex][4];
   }
   printf("\t%d", matrix[i][4]);
}
 
i++;
printf ("\n");
}
 
inFile.close ();                                         // Close the infile
 
for(i = 0; i < 10; i++)                                  // Set the counter for the genotypes
{
  assert( ( matrix[i][3] == 0  ) || ( matrix[i][3] == 1 ) ) ; 
  assert( ( matrix[i][4] == 0 ) || ( matrix[i][4] == 1 ) ) ; 
  int sum =  matrix[i][3] + matrix[i][4] ;
  if( sum == 2 ) ++counters[1][1] ;
  else if( sum == 1 ) ++counters[0][1] ;
  else ++counters[0][0] ; 
}
 
printf("\n");
printf("Cumulative genotype totals:\n");        
printf("AA: %d\n", counters[0][0]);                      // Print total number of AA individuals
printf("AB: %d\n", counters[0][1]);                      // Print total number of heterozygotes
printf("BB: %d\n", counters[1][1]);                      // Print total number of BB individuals
printf("\n");
printf("\n");
repeats++;                                               // End loop here
}
 
fclose(output_file);
 
}
 
void SetSeed() 
{
 
                                                          // Determining the seed file
     FILE *seed_file;
     long int seed_value;
 
     seed_file = fopen("seed.txt","r");                   // Open seed file
     fscanf(seed_file,"%d",&seed_value);                  // Exctract seed from file
     fclose(seed_file);                                   // Close seed file
     srand(seed_value);                                   // Randomise seed value
     seed_file = fopen("seed.txt","w");                   // Create temporary output
     fprintf(seed_file,"%d",rand());                      // Print random number to output
     fclose(seed_file);                                   // Close temporary seed output file
}
#include <fstream.h>
#include <stdlib.h>
#include <assert.h>


int i, j;
int matrix[10000][5] = {0};                              //Define a matrix with a maximum of 100 rows and 6 columns
int counters[2][2] = {0};                                // Define the genotype counter     
int repeats = 0;
int norepeats;
float p, q;
float rand1, rand2, rand3, rand4;
void SetSeed();

int main () {

FILE *output_file = fopen("output.txt", "w");

printf("Enter the frequency of allele A: ");
scanf("%f", &p);
printf("\n");
printf("Frequency of allele A (p) is: %.3f\n", p);       // States the frequency of the A allele
q = 1 - p;                                               // The value of q is 1 - (the probability entered for p)

printf("Frequency of allele B (q) is: %.3f\n", q);       // States the frequency of the B allele
printf("\n");
printf("Please enter the desired number of repeats: ");
scanf("%d", &norepeats);                                 // Desired number of repeats of the program stored in 'norepeats'
printf("\n");

while (repeats != norepeats){                            // A while loop to loop the program 'norepeats' amount of times

const float RANGE = 1.0;                                 // Random number generated is below 1
SetSeed();                                               // Seed file for RNG set here

//Open the input file//
ifstream inFile;
inFile.open("input.txt");                                // Genealogy input file opened

  if (!inFile)
  {
  printf ("Unable to open input file");                  // Error message reported if input.txt cannot be opened
  exit(1);
  }

//Read the input file into the array
while (inFile >> matrix[i][0])
{
printf ("%d\t", matrix[i][0]);
for (j = 1; j < 3; j++)
{
inFile >> matrix[i][j];
printf ("%d\t", matrix[i][j]);
}

int counter;

if (matrix[i][1] == 0 && matrix[i][2] == 0){             // If the individual is a founder:
  
   rand1 = (float) rand() * RANGE / RAND_MAX;            // Random number 1 generated 
   rand2 = (float) rand() * RANGE / RAND_MAX;            // Random number 2 generated
   
   if (rand1 < p){                                       // Place a 0 allele down in column 4 if random number 1 is below the set p value
   matrix[i][3] = 0;
   }   
   else{
   matrix[i][3] = 1;                                     // Place a 1 allele down in column 4 if random number 1 is above the set p value
   }      
   printf("\t%d", matrix[i][3]);
   

   if (rand2 < p){                                       // Place a 0 allele down in column 5 if random number 2 is below the set p value
   matrix[i][4] = 0;
   }      
   else{                                                 // Place a 1 allele down in column 5 if random number 2 is above the set p value
   matrix[i][4] = 1;
   }
   printf("\t%d", matrix[i][4]);
   }
   
else{
   int dad = matrix[i][1];                               // 1 is "dad" column
   int mum = matrix[i][2];                               // 2 is "mum" column

   int dadRowIndex = dad - 1;                            // The row of the father is 'dad - 1' as the first row is set at zero
   int mumRowIndex = mum -1;                             // The row of the mother is 'mum - 1' as the first row is set at zero

   for (counter = 1;counter <= 1;counter++){
   rand3 = (float) rand() * RANGE / RAND_MAX;            // Random number 3 generated
   rand4 = (float) rand() * RANGE / RAND_MAX;            // Random number 4 generated
   }
   if (rand3 < 0.5){                                     // If random number 3 is less than a half, receive allele stored in column 4 from dad
   matrix[i][3] = matrix[dadRowIndex][3];
   }   
   else{                                                 // If random number 3 is more than a half, receive allele stored in column 5 from dad
   matrix[i][3] = matrix[dadRowIndex][4];
   }
   printf("\t%d", matrix[i][3]);
      
   if (rand4 < 0.5){                                     // If random number 4 is less than a half, receive allele stored in column 4 from mum
   matrix[i][4] = matrix[mumRowIndex][3];
   }
   else{                                                 // If random number 4 is more than a half, receive allele stored in column 5 from mum
   matrix[i][4] = matrix[mumRowIndex][4];
   }
   printf("\t%d", matrix[i][4]);
}

i++;
printf ("\n");
}

inFile.close ();                                         // Close the infile

for(i = 0; i < 10; i++)                                  // Set the counter for the genotypes
{
  assert( ( matrix[i][3] == 0  ) || ( matrix[i][3] == 1 ) ) ; 
  assert( ( matrix[i][4] == 0 ) || ( matrix[i][4] == 1 ) ) ; 
  int sum =  matrix[i][3] + matrix[i][4] ;
  if( sum == 2 ) ++counters[1][1] ;
  else if( sum == 1 ) ++counters[0][1] ;
  else ++counters[0][0] ; 
}

printf("\n");
printf("Cumulative genotype totals:\n");        
printf("AA: %d\n", counters[0][0]);                      // Print total number of AA individuals
printf("AB: %d\n", counters[0][1]);                      // Print total number of heterozygotes
printf("BB: %d\n", counters[1][1]);                      // Print total number of BB individuals
printf("\n");
printf("\n");
repeats++;                                               // End loop here
}

fclose(output_file);

}
 
void SetSeed() 
{
  
                                                          // Determining the seed file
     FILE *seed_file;
     long int seed_value;

     seed_file = fopen("seed.txt","r");                   // Open seed file
     fscanf(seed_file,"%d",&seed_value);                  // Exctract seed from file
     fclose(seed_file);                                   // Close seed file
     srand(seed_value);                                   // Randomise seed value
     seed_file = fopen("seed.txt","w");                   // Create temporary output
     fprintf(seed_file,"%d",rand());                      // Print random number to output
     fclose(seed_file);                                   // Close temporary seed output file
}

Result:

Desired number of repeats = 3

1 0 0 0 1
2 0 0 1 1
3 0 0 0 1
4 1 2 1 1
5 1 2 1 1
6 0 0 1 0
7 3 4 0 1
8 5 6 1 1
9 7 8 1 1
10 7 8 0 1

Cumulative totals:
00 = 0
10 = 5
11 = 5

1 0 0 0 0
2 0 0 1 0
3 0 0 0 1
4 1 2 1 1
5 1 2 1 1
6 0 0 0 1
7 3 4 1 1
8 5 6 1 1
9 7 8 1 1
10 7 8 1 1

Cumulative totals:
00 = 0
10 = 10
11 = 10

1 0 0 0 0
2 0 0 0 1
3 0 0 0 1
4 1 2 1 1
5 1 2 0 1
6 0 0 1 1
7 3 4 0 1
8 5 6 1 0
9 7 8 0 1
10 7 8 1 1

Cumulative totals:
00 = 0
10 = 15
11 = 15

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Re: Counter help

#19

Mar 27th, 2008

This bit:

 Help with Code Tags 
 C++ Syntax (Toggle Plain Text) 
         else{
            int dad = matrix[i][1];                               // 1 is "dad" column
            int mum = matrix[i][2];                               // 2 is "mum" column
 
            int dadRowIndex = dad - 1;                            // The row of the father is 'dad - 1' as the first row is set at zero
            int mumRowIndex = mum -1;                             // The row of the mother is 'mum - 1' as the first row is set at zero
 
            for (counter = 1;counter <= 1;counter++){
               rand3 = (float) rand() * RANGE / RAND_MAX;            // Random number 3 generated
               rand4 = (float) rand() * RANGE / RAND_MAX;            // Random number 4 generated
            }
            if (rand3 < 0.5){                                     // If random number 3 is less than a half, receive allele stored in column 4 from dad
               matrix[i][3] = matrix[dadRowIndex][3];
            }   
            else{                                                 // If random number 3 is more than a half, receive allele stored in column 5 from dad
               matrix[i][3] = matrix[dadRowIndex][4];
            }
            printf("\t%d", matrix[i][3]);
 
            if (rand4 < 0.5){                                     // If random number 4 is less than a half, receive allele stored in column 4 from mum
               matrix[i][4] = matrix[mumRowIndex][3];
            }
            else{                                                 // If random number 4 is more than a half, receive allele stored in column 5 from mum
               matrix[i][4] = matrix[mumRowIndex][4];
            }
            printf("\t%d", matrix[i][4]);
         }
         else{
            int dad = matrix[i][1];                               // 1 is "dad" column
            int mum = matrix[i][2];                               // 2 is "mum" column

            int dadRowIndex = dad - 1;                            // The row of the father is 'dad - 1' as the first row is set at zero
            int mumRowIndex = mum -1;                             // The row of the mother is 'mum - 1' as the first row is set at zero

            for (counter = 1;counter <= 1;counter++){
               rand3 = (float) rand() * RANGE / RAND_MAX;            // Random number 3 generated
               rand4 = (float) rand() * RANGE / RAND_MAX;            // Random number 4 generated
            }
            if (rand3 < 0.5){                                     // If random number 3 is less than a half, receive allele stored in column 4 from dad
               matrix[i][3] = matrix[dadRowIndex][3];
            }   
            else{                                                 // If random number 3 is more than a half, receive allele stored in column 5 from dad
               matrix[i][3] = matrix[dadRowIndex][4];
            }
            printf("\t%d", matrix[i][3]);

            if (rand4 < 0.5){                                     // If random number 4 is less than a half, receive allele stored in column 4 from mum
               matrix[i][4] = matrix[mumRowIndex][3];
            }
            else{                                                 // If random number 4 is more than a half, receive allele stored in column 5 from mum
               matrix[i][4] = matrix[mumRowIndex][4];
            }
            printf("\t%d", matrix[i][4]);
         }

I'm not sure what it's supposed to do, but I suspect it's going back and changing some of the allele values in previous rows. So, what you display upon assignment is not always the value still there when you get to the counting portion. If you put a loop to display the matrix just before the counting loop, you'll see this occurs.

 Help with Code Tags 
 C++ Syntax (Toggle Plain Text) 
      for( int r = 0; r < 10; r++ )
      {
         for( int c = 0; c < 5; c++ )
            cout << matrix[r][c] << "  " ;
         cout << endl;
      }
 
 
      for(i = 0; i < 10; i++)                                  // Set the counter for the genotypes
      {
         assert( ( matrix[i][3] == 0  ) || ( matrix[i][3] == 1 ) ) ; 
         assert( ( matrix[i][4] == 0 ) || ( matrix[i][4] == 1 ) ) ; 
         int sum =  matrix[i][3] + matrix[i][4] ;
         if( sum == 2 ) ++counters[1][1] ;
         else if( sum == 1 ) ++counters[0][1] ;
         else ++counters[0][0] ; 
      }
      for( int r = 0; r < 10; r++ )
      {
         for( int c = 0; c < 5; c++ )
            cout << matrix[r][c] << "  " ;
         cout << endl;
      }


      for(i = 0; i < 10; i++)                                  // Set the counter for the genotypes
      {
         assert( ( matrix[i][3] == 0  ) || ( matrix[i][3] == 1 ) ) ; 
         assert( ( matrix[i][4] == 0 ) || ( matrix[i][4] == 1 ) ) ; 
         int sum =  matrix[i][3] + matrix[i][4] ;
         if( sum == 2 ) ++counters[1][1] ;
         else if( sum == 1 ) ++counters[0][1] ;
         else ++counters[0][0] ; 
      }

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Re: Counter help

#20

Mar 27th, 2008

•

Originally Posted by andyg55

Result:

Desired number of repeats = 3

1 0 0 0 1
2 0 0 1 1
3 0 0 0 1
4 1 2 1 1
5 1 2 1 1
6 0 0 1 0
7 3 4 0 1
8 5 6 1 1
9 7 8 1 1
10 7 8 0 1

Cumulative totals:
00 = 0
10 = 5
11 = 5

1 0 0 0 0
2 0 0 1 0
3 0 0 0 1
4 1 2 1 1
5 1 2 1 1
6 0 0 0 1
7 3 4 1 1
8 5 6 1 1
9 7 8 1 1
10 7 8 1 1

Cumulative totals:
00 = 0
10 = 10
11 = 10

1 0 0 0 0
2 0 0 0 1
3 0 0 0 1
4 1 2 1 1
5 1 2 0 1
6 0 0 1 1
7 3 4 0 1
8 5 6 1 0
9 7 8 0 1
10 7 8 1 1

Cumulative totals:
00 = 0
10 = 15
11 = 15

These are the actual results or the desired results?
The results of the second group (non-cumulative) should be this, correct?

 Help with Code Tags 
 C++ Syntax (Toggle Plain Text) 
0 0 0 0
0 0 1 0
0 0 0 1
1 2 1 1
1 2 1 1
0 0 0 1
3 4 1 1
5 6 1 1
7 8 1 1
7 8 1 1
 
Non-Cumulative totals:
= 1 (row 1)
= 3 (rows 2, 3, 6)
= 6 (rows 4, 5, 7, 8, 9, 10)
0 0 0 0
0 0 1 0
0 0 0 1
1 2 1 1
1 2 1 1
0 0 0 1
3 4 1 1
5 6 1 1
7 8 1 1
7 8 1 1

Non-Cumulative totals:
= 1 (row 1)
= 3 (rows 2, 3, 6)
= 6 (rows 4, 5, 7, 8, 9, 10)

Is that right? So 01 and 10 are the same result, correct? Or are they considered different, in which case you should have four totals rows, not three?

The first 3 columns are irrelevant to these totals, right? We are only looking at columns 4 and 5.

Note: I picked the second group since the first had no 00 rows. Also, do you want to display the current round's tallies in addition to the cumulative or just the cumulative tallies, as you have?

Last edited by VernonDozier; Mar 27th, 2008 at 7:40 pm. Reason: math error