large textfile 27580*1102 cell

fid = fopen('Cancer.txt','r');
data={};
while ~feof(fid)
  l=fgetl(fid);   %get the lines
    if isempty(strfind(l,'NA')),  %remove NA rows
    else 
        continue
    end
        %read next line
     idx=regexp(l,'\t','split');   %split the colmuns of this line which don't have NA and look for ';' in every column and split it 
      [nrow,ncol]=size(idx);  
      for i=1:ncol  
                if idx(i)==';'   %look for columns which have ';'and split it 

                split this column into 2 columns and put the second column
                       into a new row
                        idx = regexp(idx,';','split')
                        l=[{l(1:idx-1)}; {[l(1:itab) l(idx+1:end)]}]; %split the line into 2
                end
                      i=i+1;
             end

            fprintf(fid,l,idx);
  end
  fid=fclose(fid);

inputs:

Hybridization REF  TCGA-A6-2672-11A-01D-1551-05  TCGA-A6-2672-11A-01D-1551-05  TCGA-A6-2672-11A-01D-1551-05
Composite Element REF  Beta_value  Gene_Symbol  Chromosome  Genomic_Coordinate  Beta_value  Gene_Symbol
cg00000292  0.511852232819811  ATP2A1  16  28890100  0.787687855895422  ATP2A1
cg00003994  0.0341977140819682    MEOX2   15725862  0.334815614333325     MEOX2
cg00008493  0.987979722052904  "COX8C;KIAA1409"  14  93813777  0.986128428295584  "COX8C;KIAA1409"
cg00011459  0.922491239231445  "TMEM186;PMM2"  16  8890425  0.961124285303233  "TMEM186;PMM2"

output:

Hybridization REF  TCGA-A6-2672-11A-01D-1551-05  TCGA-A6-2672-11A-01D-1551-05  TCGA-A6-2672-11A-01D-1551-05 ……
cg00000292  0.511852232819811  ATP2A1   0.787687855895422  
cg00003994  0.0341977140819682    MEOX2   0.334815614333325     
cg00008493  0.987979722052904  COX8C     0.986128428295584      
cg00008493  0.987979722052904  KIAA1409  0.986128428295584

[Rik]

I don't even see a question to be answered. Have a read here for a guide about how to increase the likelihood of a fast answer.

[chocho]

i have a large textfile (27581*1102) and i want to read it line by line and save it to new file i have posted the code and the input of this text file and which output i want to get

[chocho]

textfile have these informations:

Hybridization REF  TCGA-A6-2672-11A-01D-1551-05  TCGA-A6-2672-11A-01D-1551-05  TCGA-A6-2672-11A-01D-1551-05
Composite Element REF  Beta_value  Gene_Symbol  Chromosome  Genomic_Coordinate  Beta_value  Gene_Symbol
cg00000292  0.511852232819811  ATP2A1  16  28890100  0.787687855895422  ATP2A1
cg00003994  0.0341977140819682    MEOX2   15725862  0.334815614333325     MEOX2
cg00008493  0.987979722052904  "COX8C;KIAA1409"  14  93813777  0.986128428295584  "COX8C;KIAA1409"
cg00011459  0.922491239231445  "TMEM186;PMM2"  16  8890425  0.961124285303233  "TMEM186;PMM2"
.......................................................................

i want to get this output :

Hybridization REF  TCGA-A6-2672-11A-01D-1551-05  TCGA-A6-2672-11A-01D-1551-05  TCGA-A6-2672-11A-01D-1551-05 ……
cg00000292  0.511852232819811  ATP2A1   0.787687855895422  
cg00003994  0.0341977140819682    MEOX2   0.334815614333325     
cg00008493  0.987979722052904  COX8C     0.986128428295584      
cg00008493  0.987979722052904  KIAA1409  0.986128428295584

[chocho]

Appreciate your help!

Answer 1

[Rik]

So essentially you have a tab separated file, where you only want to keep specific columns.

You can read a file like this with readtable. If you really have to go through it line-by-line you can use a for loop, but with this syntax you should be able to select the columns you want to keep. (and with writetable you can write the new file)

Note1: You can set the 'Delimiter' parameter to a tab with '\t'.

Note2: You'll need Matlab 2013b or later. Otherwise you'll have to muck about with the textscan function.

[chocho]

i have R2012a

[chocho]

i used fopen and how to select the columns to keep and i have around 1102 columns , do i have to specify them coltokeep=[2 3 6 10 14 18 22 26 ......]

[Rik]

I would say so, yes. I would exploit any regularity I could find, so does this fit your columns: [2 3 6:4:end]?

[chocho]

 yeah i want like this then from those 6:4:end , i want to calculate the average between them because all of them are of type float
so plz could you help me to do that it seems for me to hard to do it .
i really appreciate your help

[Rik]

If you have managed to convert your data to a matrix, then you can use the command mean(data,2) to get the average along the 2nd dimension (so the columns)