Read text file lines and analyze

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Lmm3
Lmm3 2017-7-24
回答： OCDER 2017-9-9
I would appreciate help with reading and analyzing a text file. The text file (rosalind_gc1.txt) is in this format:
>Rosalind_4949
ACTTCTATGTAGCGCGCTATTTCAAGGGATCGGCCAATAGTACGACGTGTTTCATCTAGT GCGACAAATGTATATACCGTTTTCATTACGTACCACGATAAGTTGAAGCCCGTATTC AGACGCGGGAGCCGTCTGCTGGACAAGTACTAGCTGGTCCATCCTCCCCACCAAAGGGAA
>Rosalind_7490
AACTGGGAATTTCTATATTGGGCGGTAAGCTCGGGGCAATCTATTAGTTGAATGCAACAG TAACAAACTTGCCGTCGGTCGCTGTTCGCGCAGCATTAATAATAACTCTGGCGAGTAGAT
>Rosalind_8337
CCTTGTTGTCTACCCACCAAGTCAGATAGACAGTTGGCTGTCTCCAACGCAGATTTTCTA CGCTTCATGCTCTTGCGACTCATGTCGCCTGGGTTTATTGCTTCTCTACGGGATAACCGC CCGGGCTCACTCTACCCGCGGGAAGGCCGCCCTCTCTCCCGTGTGCCTACATAA
I would like to determine the %GC for the data sets between each “>Rosalind” heading. For example, in the example above there are 3 data sets. The %GC for the text between “>Rosalind_4949” and “>Rosalind_7490” is 48.5876% and between “>Rosalind_7490” and “>Rosalind_8337” is 45.000%.
I’m trying to use the following code but I don’t know how to read the lines as blocks between each “>” and I don’t know how to concatenate the lines as I read them. I would appreciate any help.
fid = fopen('rosalind_gc1.txt');
while ~feof(fid)
templine = fgetl(fid);
a = strcmp(templine, '>');
if a == 0
G = length(strfind(templine,'G'));
C = length(strfind(templine,'C'));
z = length(templine);
%Per = (G+C)*100/z
end
end
Per = (G+C)*100/z

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采纳的回答

Lmm3
Lmm3 2017-9-9
The following code is what I used to read from the data file and determine %GC:
fid = fopen('rosalind_gc.txt');
n = 1;
G = 0;
C = 0;
z = 1;
while ~feof(fid)
templine = fgetl(fid);
a = strfind(templine, '>');
TF = isempty(a);
if TF == 1;
n= n+1;
G(1) = 0;
C(1) = 0;
z(1) = 0;
G(n) = length(strfind(templine,'G'));
C(n) = length(strfind(templine,'C'));
z(n) = length(templine);
G(n) = G(n) + G(n-1);
C(n) = C(n) + C(n-1);
z(n) = z(n) + z(n-1);
continue
% Per(n) = (G(n)+C(n))*100/z(n)
else TF == 0 ;
Per = (G(end)+C(end))*100/z(end)
disp(templine)
G(:,:) = [];
C(:,:) = [];
z (:,:)=[];
continue
end
end
Per =(G(end)+C(end))*100/z(end)

更多回答（2 个）

KSSV
KSSV 2017-7-24
编辑：KSSV 2017-7-24
Let data.txt be your text file...You can count the number of G in your file as below:
fid = fopen('data.txt') ;
S = textscan(fid,'%s','delimiter','\n') ;
fclose(fid) ;
S = S{1} ;
N = 0 ;
for i = 1:length(S)
N = N+length(strfind(S{i}, 'G'));
end
Without loop :
fid = fopen('data.txt') ;
S = textscan(fid,'%s','delimiter','\n') ;
fclose(fid) ;
S = S{1} ;
Ni = strfind(S,'G') ;
N = sum(cellfun(@numel,Ni)) ;
  1 个评论
Lmm3
Lmm3 2017-7-25
KSSV thank you for your response. Could you explain to me what the line S = S{1} is doing? The code returns the total number of "G" occurrences for the data file, but do you have a suggestion how to get the "G" occurrences between each of the headers that begin with ">Rosalind"? For example, in the data set above, I would like to get 3 values, the number of G occurrences between (“>Rosalind_4949” and “>Rosalind_7490”) between (“>Rosalind_7490” and “>Rosalind_8337”) and G occurrences below (">Rosalind_8337).

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OCDER
OCDER 2017-9-9
If you deal with a lot of fasta files, look into fastaread (Matlab Bioinformatics Toolbox) or readFasta (a code I made for another project).
Also, cellfun and regexp become pretty handy tools.
To get GC %:
[Header, Seq] = readFasta('Seq.txt');
PercGC = cellfun(@(S)length(regexpi(S, 'G|C'))/length(S)*100, Seq);
PercGC =
48.5876
45.0000
55.1724

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