reading a file in matlab
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hello,
I have a file like below named file.txt
> head(myfile,1:4])
AT1G01060 AT1G01170 AT1G01260 AT1G01380
AT1G01060 1.00000000 0.3885284 -0.14720327 -0.01865947
AT1G01170 0.38852841 1.0000000 -0.29069241 0.26992353
AT1G01260 -0.14720327 -0.2906924 1.00000000 0.30973373
AT1G01380 -0.01865947 0.2699235 0.30973373 1.00000000
AT1G01490 0.24681279 0.3955740 -0.07497821 0.23271890
AT1G01500 0.05720335 -0.1786700 -0.26813919 -0.60440141
> dim(myfile)
[1] 2885 2885
please someone help me to read this file in matlab I was really exhausted
thank you
9 Comments
per isakson
on 12 Feb 2016
Edited: per isakson
on 13 Feb 2016
Yes, ND.m takes a square double array and no strings. Try the code in my answer. It should read files like tRMA.txt regardless of the number of columns and rows.
Accepted Answer
per isakson
on 12 Feb 2016
Edited: per isakson
on 15 Feb 2016
- I failed to read tRMA.txt with Import Data. It choked Matlab (R2013a)
- The code below reads the file, tRMA.txt.
- I was a little surprised to see that num isn't square.
fid = fopen('tRMA.txt');
str = fgetl( fid );
[~] = fclose( fid );
colhead = strsplit( str, '\t' );
ncolumn = length( colhead );
fid = fopen('tRMA.txt');
fmt = ['%s',repmat('%f',[1,ncolumn])];
cac = textscan( fid, fmt, 'Headerlines',1, 'Delimiter','\t', 'CollectOutput',true );
[~] = fclose( fid );
rowhead = cac{1,1};
num = cac{1,2};
whos colhead rowhead num
outputs
Name Size Bytes Class Attributes
colhead 1x2885 375050 cell
num 164x2885 3785120 double
rowhead 164x1 22632 cell
 
In responce to comments:
I have converted the script to a function, preND. Functions are easier to use than scripts. Run
>> [ M, colhead, rowhead ] = preND( 'correlation.txt' );
>> mat_nd = ND( M );
>> imagesc( mat_nd )
where
function [ M, colhead, rowhead ] = preND( filespec )
fid = fopen( filespec );
str = fgetl( fid );
[~] = fclose( fid );
colhead = strsplit( str, '\t' );
ncolumn = length( colhead );
fid = fopen( filespec );
fmt = ['%s',repmat('%f',[1,ncolumn])];
cac = textscan( fid, fmt, 'Headerlines',1 ...
, 'Delimiter','\t', 'CollectOutput',true );
[~] = fclose( fid );
rowhead = cac{1,1};
M = cac{1,2};
end
the result is
![](https://www.mathworks.com/matlabcentral/answers/uploaded_files/172836/image.png)
 
The names of the rows and the columns are in the cell arrays, rowhead and colhead.
9 Comments
per isakson
on 16 Feb 2016
Replace
colhead = strsplit( str, '\t' );
by
colhead = regexp( str, '\t', 'split' );
More Answers (2)
Walter Roberson
on 12 Feb 2016
fid = fopen('tRMA.txt, 'rt');
%All columns are tab separated, but there is no initial tab before the first gene row
%header which corresponds to the second column of input for the rest of the file,
%with the first column of input being a row name string
header = fgetl(fid);
col_names = regexp(header, '\t\, 'split');
num_cols = length(col_names);
fmt = ['%s', repmat('\t%f', 1, num_cols)];
datacell = textscan(fid, fmt, 'CollectOutput', 1, 'Delimiter', '\t');
fclose(fid);
row_names = datacell{1};
cor = datacell{2};
Now there is row_names (a cell array of strings), col_names (a cell array of strings), and cor (a rectangular numeric matrix)
0 Comments
A Mugesh
on 24 Apr 2019
Hi,
I am a beginer in mat lab learning, i want to know the code how to read the different format of files in matlab....
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