Searching the contents of a file with items in a second file

I have two files - File1.txt and File2.txt. I'm searching the first column of File 1 with items from File2.

File1.txt (tab-delemited):
Ex_efxb 0.0023
MSeef 2.3000
F_ecjc 0.3338
MWEEI -0.111
DDAIij 17.777

File2.txt
MSeef
F_ecjc

Required output: The following were found in File 1:

MSeef 2.3000 F_ecjc 0.3338

I have the following script which is not giving the right output, instead it says items not found. clear all; clc;

fid  = fopen('File1.txt')
if fid ==-1
   disp('Reaction_Flux file open not successful')
else
   % Read characters and numbers into separate elements
   % in a cell array
   rxn_flux = textscan(fid,'%s %f');
   A = rxn_flux{1};
   B = rxn_flux{2};
   len1 = size(A);

     closeresult1 = fclose(fid);
     if closeresult1 == 0
         disp('Reaction_Flux file close successful')
     else
         disp('Reaction_Flux file close not successful')
     end
  end   
fid  = fopen('File2.txt')
if fid ==-1
   disp('Flux file open not successful')
else
   % Read characters and numbers into separate elements
   % in a cell array
   [rxn] = textread('File2.txt','%s');
   %rxn = textscan(fid,'%s');
   C = rxn;
   len2 = size(C);

     closeresult1 = fclose(fid);
     if closeresult1 == 0
         disp('Reaction_Flux file close successful')
     else
         disp('Reaction_Flux file close not successful')
     end
  end   
found = 0;
for i = 1:len1
    RXNFLUX = strcmpi(A(i),C);
    if RXNFLUX
        found = 1;
        break
    end
end

if found
    data = [];
    for k = 1:len1
        for m = 1:len2
                data = [data; A(k),C(m)]
            %print to file
            fprintf(data,'%s\t %d\n','Out.txt');  
        end
    end
else
    disp('rxn not found')
end

Can anyone help? Thanks

Answer 1

[Andrew Newell]

The explanation: strcmpi does a case-insensitive match (if you want case-sensitive, change to strcmp ) and returns a logical array with value 1 for every element of A that matches C{i} and 0 for every element that does not. The vertical line means "or", so if an element of RXNFLUX is already 1, it stays 1; but if it is 0 and strcmpi finds a match, it is reset to 1. For example, initially RXNFLUX is all zeros. After the first iteration, it is [0; 1; 0; 0; 0] because MSeef is the second element in A. After the second iteration, the output of the search is [0; 0; 1; 0; 0] because F_ecjc is the third element of A. Combining this with RXNFLUX using "or" gives [0; 1; 1; 0; 0].

The line

iLines = find(RXNFLUX);

finds the indices of all the elements of RXNFLUX that are equal to 1.

Answer 2

[Andrew Newell]

You've got one mistake:

     len2 = length(B);

should be

     len2 = length(C);

That must have crept in when you were changing size to length.

Answer 3

[Andrew Newell]

The file reading is fine (except that it would be better to use

len1 = length(A)
len2 = length(B)

so that len1 and len2 are scalars. However, there are a lot of problems with the processing, including

1. accessing the cell array A using A(i) instead of A{i},
2. testing for string matches ( found=1 ) before you are finished searching, and
3. not opening the file Out.txt.

Note also that if you search A for elements of C instead of the reverse, you get the indices you need for the next part.

Here is code that will do the analysis:

fid = fopen('Out.txt','w');
fprintf(fid,'The following were found in File 1:\n')

RXNFLUX = false(size(A));
for i = 1:len2
  RXNFLUX = RXNFLUX | strcmpi(C{i},A);
end

if any(RXNFLUX)
  iLines = find(RXNFLUX);
  for i=1:length(iLines)
      fprintf(fid,'%s\t %d\n',A{iLines(i)}, B(iLines(i)));
  end
else
  disp('rxn not found')
end
fclose(fid);

Answer 4

[James]

Hi Andrew,

I apologise unreservedly for my very late reply. I have not been been able to log in to the site until some minutes ago. Thank you for the solution. I have connected your code section to the file reading of mine and somehow I got some errors:

     ??? Index exceeds matrix dimensions.
    Error in ==> sollutionRxnFluxFiles at 47
  RXNFLUX = RXNFLUX | strcmpi(C{i},A);

Here 's the latest code:

fid  = fopen('File1.txt')
if fid ==-1
 disp('Reaction_Flux file open not successful')
else
 % Read characters and numbers into separate elements
 % in a cell array
 rxn_flux = textscan(fid,'%s %f');
 A = rxn_flux{1};
 B = rxn_flux{2};
 len1 = length(A);
   closeresult1 = fclose(fid);

     if closeresult1 == 0
         disp('Reaction_Flux file close successful')
     else
         disp('Reaction_Flux file close not successful')
     end
  end 
    fid  = fopen('File2.txt')
if fid ==-1
   disp('Flux file open not successful')
else
   % Read characters and numbers into separate elements
   % in a cell array
   [rxn] = textread('File2.txt','%s');
   %rxn = textscan(fid,'%s');
   C = rxn;
   len2 = length(B);
     closeresult1 = fclose(fid);
     if closeresult1 == 0
         disp('Reaction_Flux file close successful')
     else
         disp('Reaction_Flux file close not successful')
     end
  end 
    fid = fopen('Out.txt','w');
fprintf(fid,'The following were found in File 1:\n')
    RXNFLUX = false(size(A));
for i = 1:len2
  RXNFLUX = RXNFLUX | strcmpi(C{i},A);
end  
    if any(RXNFLUX)
  iLines = find(RXNFLUX);
  for i=1:length(iLines)
      fprintf(fid,'%s\t %d\n',A{iLines(i)}, B(iLines(i)));
  end
else
  disp('rxn not found')
end
fclose(fid);

Thanks!

Answer 5

[James]

Now, it works beautifully! Many thanks, Andrew.

Do you mind explaining this bit of code?

    for i = 1:len2
  RXNFLUX = RXNFLUX | strcmpi(C{i},A);
end