hi guys , i want to read a text file line by line and remove the lines which have NA and the duplicated columns

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chocho 2017-2-15

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此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/325176-hi-guys-i-want-to-read-a-text-file-line-by-line-and-remove-the-lines-which-have-na-and-the-duplica

编辑： Walter Roberson 2017-2-20

采纳的回答： dpb

COADREAD_methylation.txt

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d = fopen('COADREAD_methylation.txt','r');
this_line=0;
all={};
while this_line~=-1
 % C= textscan( d, '%f%s'  ) ;
    this_line=fgetl(d);
   if this_line~=-1
       all=[all;this_line];
   end
end
fclose(d);

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Stephen23 2017-2-17

编辑：Stephen23 2017-2-17

采纳的回答

dpb 2017-2-15

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此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/325176-hi-guys-i-want-to-read-a-text-file-line-by-line-and-remove-the-lines-which-have-na-and-the-duplica#answer_254913

编辑：dpb 2017-2-16

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Well, 'NA' is easy, not sure what defines the repeated columns; not enough time at present to try to parse that input file to figure out what is/isn't unique without a description being supplied...

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);

If the presence of 'NA' is all that's needed to get all the offending records, then you're done; otherwise need more details on how to tell so folks here don't have to try to work it out on their own.

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chocho 2017-2-20

编辑：Walter Roberson 2017-2-20

在 MATLAB Online 中打开

hi friend, i want to make this code like this format

Note: i want to get every line and check if it has a NA remove it and get the second line, if not ckeck the columns of this line and see which column have ';' split this column and make 2 rows

fid = fopen('COADREAD_methylation.txt','r');
data={};
while ~feof(fid)
  l=fgetl(fid);   %get the lines
    if isempty(strfind(l,'NA')),  %remove NA rows
    else 
        %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
                      %D = 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
            save this line % this line will have no NA and if have ; will be splitted
      end
  end
  fid=fclose(fid);

chocho 2017-2-20

编辑：Walter Roberson 2017-2-20

在 MATLAB Online 中打开

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
cg00002426  0.519102187746053  SLMAP    3  57743543  0.932889308560864  SLMAP
cg00006414  NA  "ZNF425;ZNF398"  7  148822837  NA  "ZNF425;ZNF398"  
cg00008493  0.987979722052904  "COX8C;KIAA1409"  14  93813777  0.986128428295584      "COX8C;KIAA1409"  
cg00011459  0.922491239231445  "TMEM186;PMM2"  16  8890425  0.961124285303233  "TMEM186;PMM2"

outputs:

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  
cg00002426  0.519102187746053  SLMAP       0.932889308560864  
cg00008493  0.987979722052904  COX8C     0.986128428295584      
cg00008493  0.987979722052904  KIAA1409  0.986128428295584        
cg00011459  0.922491239231445  TMEM186  0.961124285303233  
cg00011459  0.922491239231445  PMM2                0.961124285303233