Checking whether string exist in a cell and read its ID

I have a cell array called "proteins_selected" and each row is a code for a protein, looks like this:

Then I would like to translate each protein code into its ID, so i have another cell array "GoAnnotationsWithId" which is like a dictionary(the second row is ID):

So i would like to chech whether proteins from proteins_selected exist in GoAnnotationsWithId file, and get appropriate ID of this protein. I would be extremely grateful for any help.

Answer 1

[Stephen23]

The simple, efficient MATLAB approach would be to use ISMEMBER:

A = {'banana',12;'orange',23;'apple',35;'peach',74;'pear',51;'cherry',62}

A = 6×2 cell array
    {'banana'}    {[12]}
    {'orange'}    {[23]}
    {'apple' }    {[35]}
    {'peach' }    {[74]}
    {'pear'  }    {[51]}
    {'cherry'}    {[62]}

B = {'apple','bldf','orange'}

B = 1×3 cell array
    {'apple'}    {'bldf'}    {'orange'}

[X,Y] = ismember(B,A(:,1));
V = nan(size(X));
V(X) = [A{Y(X),2}]

V = 1×3

35 NaN 23

[DGM]

Yeah, that's way more sensible.

Answer 2

[DGM]

Something like this may work

LUT = {'banana',12;
       'orange',23;
       'apple',35;
       'peach',74;
       'pear',51;
       'cherry',62};

% random assortment of fruit names
mydata = LUT(randi(6,10,1),1)

% if you want the output to be a numeric vector
f = @(x) LUT{strcmp(x,LUT(:,1)),2};
output = cellfun(f,mydata)

gives

mydata =
  10×1 cell array
    {'cherry'}
    {'orange'}
    {'apple' }
    {'peach' }
    {'peach' }
    {'peach' }
    {'banana'}
    {'pear'  }
    {'cherry'}
    {'banana'}
output =
    62
    23
    35
    74
    74
    74
    12
    51
    62
    12

Alternatively:

% if you want the output to be a cell vector
f = @(x) LUT(strcmp(x,LUT(:,1)),2);
output = cellfun(f,mydata)

[M]

As I understood, in my case it should look like:

f = @(x) GoAnnotationsWithId{strcmp(x,GoAnnotationsWithId(:,1)), 2};
output = cellfun(f,proteins_selected)

Unfortunately it doesn't work for me, i got an error:

Insufficient number of outputs from right hand side of equal sign to satisfy assignment.

Error in umb_2_0 (line 61)

f = @(x) GoAnnotationsWithId{strcmp(x,GoAnnotationsWithId(:,1)), 2};

Am I doing something wrong?

[DGM]

Oh I see what's going on. The problem is that there are elements in your list that aren't in the dictionary. This complicates things. I ended up having to write a function to handle undefined cases:

LUT = {'banana',12;
       'orange',23;
       'apple',35;
       'peach',74;
       'pear',51;
       'cherry',62};

% random assortment of fruit names
mydata = [LUT(randi(6,10,1),1); {'bldf'}]

% if you want the output to be a numeric vector
f = @(x) actualfunction(x,LUT);
output = cellfun(f,mydata)

function out = actualfunction(x,LUT)
    m = strcmp(x,LUT(:,1));
    if any(m)
        out = LUT{m,2};
    else
        out = NaN; % or whatever default value you want
    end
end

There may be more elegant ways of doing this.

If it turns out that these problem entries are to be discarded anyway, you could also do this instead.

% if you only want to keep valid entries
f = @(x) any(strcmp(x,LUT(:,1)));
mydata = mydata(cellfun(f,mydata)); % get rid of bad entries
f = @(x) LUT{strcmp(x,LUT(:,1)),2};
output = cellfun(f,mydata) % do lookup like first example

I doubt it's as fast or faster, but it's more compact.