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
chocho 2017-2-15
编辑： Walter Roberson 2017-2-20
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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dpb
dpb 2017-2-15
编辑：dpb 2017-2-16
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
chocho 2017-2-20
编辑：Walter Roberson 2017-2-20
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
chocho 2017-2-20
编辑：Walter Roberson 2017-2-20
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
appreciate your help !

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