How can I save the beginning and end positions of each sequence in a cell array?
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Austin Shipley
el 26 de Nov. de 2020
Respondida: Rik
el 29 de Nov. de 2020
So I am looping through codons and recording them on a .txt file. The script works, but I need the sequence to begin at the starting codon position, stop at the end codon then continue through the cell array while recording all of the following start and end codon sequences. I would just like to know the best option I can use to tweak my code here. Thanks in advance!
fid = fopen("sequence_long2.txt",'r');
C = textscan(fid,'%3s');
x = C{1}
fclose(fid);
%Start sequence
ss = 1;
% end sequence
es = 183479;
seq_id = long_codon(x(ss:es));
function seq = long_codon(v)
seq = (v);
for pos = 1:length(seq)
if strcmp(seq{pos},'TAC')
index = find(strcmp(v,seq{pos}));
StartPos = index;
elseif (strcmp(seq{pos},'ACT') || strcmp(seq{pos},'ATT') || strcmp(seq{pos},'ATC'))
index = find(strcmp(v,seq{pos}));
EndPos = index;
end
end
fid2 = fopen('report_long.txt','w+');
fprintf(fid2,'Name: OP \n');
fprintf(fid2,'Lab 13: DNA Pattern Matching\n \n');
fprintf(fid2,'Start Position of Gene is: %d \n',StartPos);
fprintf(fid2, 'End Position of Gene is: %d \n',EndPos);
fclose(fid2);
end
14 comentarios
Rik
el 28 de Nov. de 2020
I would urge you to change to strfind first. Then you can loop through all start codons, removing later start codons if they are inside the gene being read.
Austin Shipley
el 28 de Nov. de 2020
Editada: Austin Shipley
el 28 de Nov. de 2020
Respuesta aceptada
Rik
el 29 de Nov. de 2020
%Since your code is working fine you can keep it as is.
%I just used my own function to use your data.
x_conv=readfile('https://www.mathworks.com/matlabcentral/answers/uploaded_files/430218/sequence_long2.txt');
x_conv=x_conv{1};
%find all possible start codons and stop codons
Start_loc = strfind(x_conv,'TAC');
End_loc = cellfun(@(stopcodon)strfind(x_conv,stopcodon),{'ATC','ACT','ATT'},'UniformOutput',false);
End_loc = horzcat(End_loc{:});
n=0;
while n<numel(Start_loc)
n=n+1;
this_start=Start_loc(n);
%select all possible end codons
this_end=End_loc(End_loc>this_start);
%figure out which is the first end codon with an offset of 3
this_end=this_end(mod(this_end-this_start,3)==0);
this_end=this_end(1);
%now we need to remove elements in Start_loc that in the current gene
Start_loc(Start_loc>this_start & Start_loc<this_end)=[];
%store the end as well
End_loc(n)=this_end;
end
%remove extra values in End_loc
End_loc((n+1):end)=[];
genes=cell(size(End_loc));
for n=1:numel(End_loc)
genes{n}=x_conv(Start_loc(n):End_loc(n));
end
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