Text file that is read into an array

[Mark44]

In post #24 you said this:

! Here is my Data (list of ALL possible amino acids
DATA /'A,C,D,E,F,G,H,I,K,L,M,N,P,Q,E,A,T,V,W,Y'/

Might have been a copy/paste mistake, but the list above has duplicates for E and A, and is missing R and S. The data file that you attached at the beginning of this thread contains numerous R's and S's. The output from my Python code in post #28 doesn't have entries for R and S, which I presume are valid amino acids. I didn't include these two because you didn't list them above.

I have to ask: Is there some reason you're doing this with Fortran? To me, using Fortran in the context of this problem is something like trying to make fine furniture using only a hammer.

 

[Mark44]

Adding R and S as possible amino acids, and tweaking the output format slightly, this is what I'm now getting. The 'Misc' category now consists only of the newline characters that were in your input textfile.

Amino acid  Count Proportion
  E    3193  9.143 %
  N    1111  3.181 %
  H    478  1.369 %
  M    398  1.140 %
  W    466  1.334 %
  I    2062  5.905 %
  Q    942  2.697 %
  A    2084  5.968 %
  K    2943  8.427 %
  Y    999  2.861 %
  D    1720  4.925 %
  L    2117  6.062 %
  C    513  1.469 %
  S    2463  7.053 %
  Misc   572  1.638 %
  G    2066  5.916 %
  T    2546  7.291 %
  F    908  2.600 %
  P    2517  7.207 %
  V    3184  9.117 %
  R    1640  4.696 %
Cumulative total percentages: 100.00%
Characters processed:  34922

 

[Sue Parks]

This is a practice simulation in fortran. I have a good foundation in Python. We (YOU & I) know Fortran is not the best way to go about solving this problem, but it can be done.

 

[Mark44]

This is a practice simulation in fortran. I have a good foundation in Python. We (YOU & I) know Fortran is not the best way to go about solving this problem, but it can be done.

Sure.

Here's what you posted earlier:

subroutine AAFrequencyTitin

Integer:: countA  , averageA  , countC , countD, average D
do i =1, len(String)
    if ( String == 'A')
        countA = countA + 1
        averageA = countA/sumAminoAcids
       
    else if (String == 'D')
        countD = countD + 1
        averageD = countD/sumAminoAcids
    
end do
end subroutine AAFrequencyTitin[/quote]
Something like this will work, but it needs some work.
1. The subroutine should have at least one parameter, the string (CHARACTER* xxxxx) that was read earlier in another subroutine.
2. You could use countA, countC, countD, etc to store the counts of the various amino acids, but you DON'T need separate variables for the relative frequencies. Just keep track of the total number of amino acids, and display countA/totalCount for the relative proportion of A, and so on.
3. The string (passed as a parameter) can be read one character at a time, by baseq[i:i]. Get the character in the i-th position, and run it through a chain of IF... ELSE IF ... ELSE IF ... statements, incrementing the appropriate countX when the IF clause is matched.
Once you have cycled through the string, and all of the countX variables are set, you could store these values in an array of suitable size (one-dimensional, with one cell for each amino acid count). That array could be an OUT parameter in your function, that could be used by some other subroutine, similar to what I did in my Python code.