Count number of nucleotide bases (letters) in file with multiple en... (2024)

Be much easier if you would attach a data file for folks to work with...as for hints, without a data file from which to see just what you're starting with, I'd venture using a table and @doc:rowfun or groupsummary even with grouping variables will give you the desired results directly.

% this is what the attached file contains:

type file.txt

data = readlines('file.txt');

ID = regexp(data(1:2:end),'>(.*?):','tokens','once');

ID = vertcat(ID{:});

introns = data(2:2:end);

[G,ID] = findgroups(ID);

F = @(x)sum(cellfun(@numel,x));

count = groupsummary(introns,G,F);

T = table(ID,count)

data = readlines('grp1_introns.txt');

data(strlength(data)==0)=[]; % remove blank lines, if any

data(1:12)

ix=find(startsWith(data,'>'));

dx=[diff(ix);0];

iy=find(dx>2);

whos ix dx iy

[ix(1:10) dx(1:10) iy(1:10)]

markfordelete=[]; % accumulator for marked rows

for i=1:numel(iy) % iterate over the elements that are multiple lines

l1=ix(iy(i))+1; % the first row in the group past the header

l2=l1+dx(iy(i))-2; % the last row in group

try

data(l1)=join(data(l1:l2),''); % put those rows together, no spaces

markfordelete=cat(1,markfordelete,[l1+1:l2].'); % keep list of rows to delete

catch

e=lasterror; e.message % for debugging

[i iy(i) ix(iy(i)) dx(iy(i)) l1 l2]

data(l1-1:end)

return

end

end

data(markfordelete)=[];

ix=find(startsWith(data,'>'));

height(ix)

any(diff(ix)~=2)

[Lmax,iMax]=max(dx)

L=strlength(data(2:2:end));

UL=unique(L);

numel(UL)

NL=histc(L,UL);

[UL NL]

[min(UL) max(UL)]

subplot(2,1,1)

bar(UL,NL)

set(gca,'XScale','log')

xlim([UL(1) UL(end)])

subplot(2,1,2)

bar(UL,NL)

set(gca,'XScale','log')

xlim([UL(1)-1 200])

xticks([UL(1) 20:10:50 100 200])

sum(L)

• Link

  Direct link to this comment

  https://support.mathworks.com/matlabcentral/answers/2149169-count-number-of-nucleotide-bases-letters-in-file-with-multiple-entries#comment_3251119

• Link

  Direct link to this comment

  https://support.mathworks.com/matlabcentral/answers/2149169-count-number-of-nucleotide-bases-letters-in-file-with-multiple-entries#comment_3251134

• Link

  Direct link to this comment

  https://support.mathworks.com/matlabcentral/answers/2149169-count-number-of-nucleotide-bases-letters-in-file-with-multiple-entries#comment_3250654

Open in MATLAB Online

• Link

  Direct link to this comment

  https://support.mathworks.com/matlabcentral/answers/2149169-count-number-of-nucleotide-bases-letters-in-file-with-multiple-entries#comment_3251114