remove header in file

latitude,  longitude,  wind_speed,  zonal_wind_speed,  meridional_wind_speed,  quality_flag
   15.25,     94.75,       314,      -267,       -81,    0
   15.25,     95.25,       427,      -333,      -186,    0
   15.25,     95.75,       452,      -290,      -290,    0
   15.25,     96.25,       459,      -211,      -389,    0
   15.25,     96.75,       471,       -91,      -453,    0
   15.25,     97.25,       519,         1,      -511,    0
   15.25,     97.75,     32767,     32767,     32767,    2
   15.25,     98.25,     32767,     32767,     32767,    2
   15.25,     98.75,     32767,     32767,     32767,    2
   15.25,     99.25,     32767,     32767,     32767,    2
   15.25,     99.75,     32767,     32767,     32767,    2
   15.25,    100.25,     32767,     32767,     32767,    2
   15.25,    100.75,     32767,     32767,     32767,    2
   15.25,    101.25,     32767,     32767,     32767,    2
   15.25,    101.75,     32767,     32767,     32767,    2
   15.25,    102.25,     32767,     32767,     32767,    2

[Sven]

What's your question? Do you want to read your data into matlab (without the header) or do you want to delete the first line from the file and re-save it?

[joo tan]

I want to load the data into matlab without header

Answer 1

[Walter Roberson]

fmt = repmat('%f',1,6);
fid = fopen('YourFileName.txt', 'rt');
datacell = textscan(fid, fmt, 'Delimiter', ',', 'HeaderLines', 1, 'CollectOutput', 1);
fclose(fid);
TheData = datacell{1};
clear datacell

[chocho]

i have file like that but i want to remove the second header line as follow:

Hybridization REF  TCGA-A6-2672-11A-01D-1551-05  TCGA-A6-2672-11A-01D-1551-05
Composite Element REF  Beta_value  Gene_Symbol  Chromosome  Genomic_Coordinate
cg00000292  0.511852232819811  ATP2A1  16  28890100

i want to delete the second headerline (Composite Element REF Beta_value Gene_Symbol Chromosome Genomic_Coordinate)

[Walter Roberson]

fmt = '%s%f%s%f%f';
fid = fopen('YourFileName.txt', 'rt');
header_to_keep = fgetl(fid);
datacell = textscan(fid, fmt, 'Headerlines', 1);
fclose(fid);

Composite_Element_Ref = datacell{1};
Beta_value = datacell{2};
Gene_Symbol = datacell{3};
Chromosome = datacell{4};
Genomic_Coordinate = datacell{5};

together with the whatever you want to do with the header_to_keep line, which you do not appear to want to delete.

If instead you wanted to delete both header lines, then

fmt = '%s%f%s%f%f';
fid = fopen('YourFileName.txt', 'rt');
datacell = textscan(fid, fmt, 'Headerlines', 2);
fclose(fid);

Composite_Element_Ref = datacell{1};
Beta_value = datacell{2};
Gene_Symbol = datacell{3};
Chromosome = datacell{4};
Genomic_Coordinate = datacell{5};

[chocho]

my fmt i more biger than that i just post an example among them

i used getl to get the whole lines of my text file , then i want to delete the whole lines 2

you get it ?

fid = fopen('COADREAD_methylation.txt','r');

data={};

while ~feof(fid)
  l=fgetl(fid);
  if isempty(strfind(l,'NA')), data=[data;{l}]; end

end
fid=fclose(fid);

[Walter Roberson]

 fid = fopen('COADREAD_methylation.txt','r');

 data={};
 linecount = 0;

 while ~feof(fid)
   l = fgetl(fid);
   linecount = linecount + 1;
   if linecount == 2; continue; end   %skip line 2 specifically

   if isempty(strfind(l,'NA'))
     data{end+1} = l;
    end

 end
 fid = fclose(fid);

... Or you could just use

data = strsplit( fileread('COADREAD_methylation.txt'), '\n' );
data{2} = [];

[chocho]

hi friend i tried that but it seemes there is an error if linecount == 2; next; end %skip line 2 specifically??

[Walter Roberson]

Sorry, should be continue instead of next.

[chocho]

Undefined function or variable 'next'.

[chocho]

sorry again if i bother you but now no error but the code doesn't delete the line 2 !!! still exist in the textfile

[Walter Roberson]

If you want to remove a line from the file itself, then you have to write out a new file.

fid_in = fopen('COADREAD_methylation.txt', 'r');
fid_out = fopen('new_file.txt', 'w');
L = fgets(fid_in);  %copy first line
fwrite(fid_out, L);
fgets(fid_in);      %read next line by do not copy it
while ~feof(fid_in);
  L = fgets(fid_in);
  fwrite(fid_out, L);
end
fclose(fid_in);
fclose(fid_out);

After that you would check to be sure everything worked, and then you could rename the old file to a safe place and rename the new file to the old name.

[chocho]

so sorry , again error Error using fwrite Invalid file identifier. Use fopen to generate a valid file identifier.

Error in Untitled (line 4) fwrite(fid_out, L);

[chocho]

on brief ,the text file is very large 22198x1 cell i want to remove the second line why you use fgets instead of fgetl !

[chocho]

i mean it's a cell array of size 27581*1 with NA without NA 22198*1

[Walter Roberson]

infile = 'COADREAD_methylation.txt';

try
  outfile = tempname();
catch ME
  error('Your TEMP environment variable is messed up, cannot create temporary file');
end

[fid_in, msg] = fopen(infile, 'r');
if fid_in < 0
  error('Could not open input file "%s" because: "%s"', infile, msg);
end

fid_out = fopen(outfile, 'w');
if fid_out < 0
  fclose(fid_in);
  error('Could not open temporary output file "%s" because: "%s"', outfile, msg);
end

L = fgets(fid_in);  %copy first line
fwrite(fid_out, L);
fgets(fid_in);      %read next line by do not copy it
while ~feof(fid_in);
  L = fgets(fid_in);
  fwrite(fid_out, L);
end
fclose(fid_in);
fclose(fid_out);

[pathname, name, ext] = fileparts(infile);
newname = fullfile( pathname, [name '_new' ext] );
try
  [success, msg] = movefile( outfile, newname );
catch ME
  success = false;
end
if success
  fprintf('Done! New file is at "%s"\n', newname );
else
  fprintf('Done, but could not move output file here. Look for it at "%s"\n', outfile );
end

[Walter Roberson]

You cannot write to any directory under "C:\Program Files (x86)" because MS Windows will not allow that. You need to cd to a different directory and work there.

[chocho]

oh that's why ,you know i put all the files in this directory C:\Program Files (x86)\MATLAB\R2012a thanks a lot ....