Remove intermittent text when reading in a table from a .dat file

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L. Borealis
L. Borealis on 19 Feb 2021
Commented: L. Borealis on 25 Feb 2021
Hi,
I am trying to use readtable for read in a .dat file. The file looks like this, where there could be 1 to very many entries in the columns that start with a "1'" here.
# NetMHCIIpan version 4.0
# Input is in PEPTIDE format
# Prediction Mode: EL+BA
# Threshold for Strong binding peptides (%Rank) 2%
# Threshold for Weak binding peptides (%Rank) 10%
# Allele: HLA-DPA10103-DPB10101
--------------------------------------------------------------------------------------------------------------------------------------------
Pos MHC Peptide Of Core Core_Rel Identity Score_EL %Rank_EL Exp_Bind Score_BA Affinity(nM) %Rank_BA BindLevel
--------------------------------------------------------------------------------------------------------------------------------------------
1 HLA-DPA10103-DPB10101 AAAAAAAAAAAAAAA 3 AAAAAAAAA 0.380 Sequence 0.020745 81.44 NA 0.366182 951.24 32.45
--------------------------------------------------------------------------------------------------------------------------------------------
Number of strong binders: 2 Number of weak binders: 0
--------------------------------------------------------------------------------------------------------------------------------------------
# Allele: HLA-DPA10103-DPB10201
--------------------------------------------------------------------------------------------------------------------------------------------
Pos MHC Peptide Of Core Core_Rel Identity Score_EL %Rank_EL Exp_Bind Score_BA Affinity(nM) %Rank_BA BindLevel
--------------------------------------------------------------------------------------------------------------------------------------------
1 HLA-DPA10103-DPB10201 BBBBBBBBBBBBBBBB 2 BBBBBBBBB 0.960 Sequence 0.491911 1.02 NA 0.712020 22.55 0.27 <=SB
--------------------------------------------------------------------------------------------------------------------------------------------
Number of strong binders: 2 Number of weak binders: 0
--------------------------------------------------------------------------------------------------------------------------------------------
# Allele: HLA-DPA10103-DPB10202
--------------------------------------------------------------------------------------------------------------------------------------------
Pos MHC Peptide Of Core Core_Rel Identity Score_EL %Rank_EL Exp_Bind Score_BA Affinity(nM) %Rank_BA BindLevel
--------------------------------------------------------------------------------------------------------------------------------------------
1[.......]
These columns would then start 2,3,4,[...]. I successfully use
opts = detectImportOptions('filename.dat');
opts.DataLines = [16 Inf];
opts.VariableNamesLine = 14;
readtable(fullfile('path','filename.dat',opts,'ReadVariableNames', true);
for files with a large number of columns between the ----, i.e. e.g.
# Allele: HLA-DPA10103-DPB10101
--------------------------------------------------------------------------------------------------------------------------------------------
Pos MHC Peptide Of Core Core_Rel Identity Score_EL %Rank_EL Exp_Bind Score_BA Affinity(nM) %Rank_BA BindLevel
--------------------------------------------------------------------------------------------------------------------------------------------
1 HLA-DPA10103-DPB10101 AAAAAAAAAAAAAAA 3 AAAAAAAAA 0.380 Sequence 0.020745 81.44 NA 0.366182 951.24 32.45
2 HLA-....
3 ....
....
....
50 HLA....
--------------------------------------------------------------------------------------------------------------------------------------------
Number of strong binders: 2 Number of weak binders: 0
--------------------------------------------------------------------------------------------------------------------------------------------
However, this does not work for short "fillings" and my code very much depends on being robust in either scenario.
I tried playing with the opts but did not get it to work. I would be very grateful for any advice! Maybe a method other than readtable (readtext?) is needed and then a conversion to a table? In the end I will need a table like this:
Thank you very much for your advice! I have spent a long time deleoping the code around this and this is the final part that keeps breaking...

Accepted Answer

Vimal Rathod
Vimal Rathod on 22 Feb 2021
  1 Comment
L. Borealis
L. Borealis on 25 Feb 2021
Thanks, Vimal!
I had actually seen that question but even the question description was not particularly clear to me. So I had left it. Thanks for pointing me back to it. I did use part of it in the end to come up with a working (yet not elegant) solution. Maybe it is useful to someone in the future:
S = regexp(fileread('S:\scratch\cdr1pool2pep1\out_00.dat'), '\r?\n', 'split');
S = S(~cellfun('isempty',S));
if isempty(S{end}); S(end) = []; end %regexp split leaves empty at bottom if file ended in \n which is common
nonheader = cellfun(@isempty, regexp(S, '^\s*#|^\s*-|^\s*P|^\s*N' )); %permit space before #
starts = strfind([false nonheader], [false true]);
stops = strfind([nonheader false], [true false]);
num_blocks = length(starts);
lenRows = length(starts(1):stops(1));
S_temp = cell(num_blocks,lenRows);
for K = 1 : num_blocks
S_temp(K,:) = S(starts(K):stops(K));
end
S = reshape(S_temp,[num_blocks*lenRows,1]);
writecell(S,'data.dat')
opts = detectImportOptions('data.dat');
tbl=readtable(('data.dat'),opts);

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