problem with regexp and split, and picking some cells

I have the following input:

>> data(1).Header

ans =

AF051909 |392-397:CAGCTG| |413-418:CAGGTG|

I needed to save them to cells as {'392-397', 'CAGCTG'; '413-418', 'CAGGTG';}

I so I used regexp to do so with the following code:

struKm(1).trueBinding = regexp(data(1).Header,'\s\||\:|\|','split');

this returns:

>> struKm(1).trueBinding

ans = 

      'AF051909'    '392-397'    'CAGCTG'    ''    '413-418'    'CAGGTG'    ''

as you can see there are to empty cells and I tried to find out why they are there but failed.

I also tried to ignore that and continue to picking up the cell that I need for the rest of my code which is 'CAGCTG' and 'CAGGTG'. I have this code to pick them up:

[r1,r2] = ismember(struKm(1).trueBinding,set)

it return zeros.

Can someone help with two issues please?

Regards, A.

Answer 1

[Azzi Abdelmalek]

you can maintain your code and add a line code to remove empty elements

data='AF051909 |392-397:CAGCTG| |413-418:CAGGTG|'    
s=regexp(data,'\s\||\:|\|','split');  
s(cellfun(@(x) isempty(x),s))=[]

Answer 2

[Abdulaziz]

Thank you for your reply.

I solved the issues but another is appeared.

Now,

        struKm(i).seqNam = cellstr(regexp(data(i).Header, '\s\||\:|\|','split')); % determen the seqance name heads 
        struKm(i).seqNam(cellfun(@(x) isempty(x),struKm(i).seqNam))=[];

This code is in a FOR LOOP.

the result for this code is:

ans = 

      'AF051909'    '392-397'    'CAGCTG'    '413-418'    'CAGGTG'

some seqNams contain only one Binding site (CAGCTG). for Example:

ans = 

      'M13483'    '445-450'    'CAACTG'

Now I want to pick the Binding sites only which are (CAGCTG, CAGGTG, CAACTG , ... etc)

I have another for loop that will do it. The code:

struSize = length(struKm);
tempcell = cell(1,1);

for m=1:struSize

      if (length(struKm(m).seqNam) == 3)
        resultsk.BS{m} = struKm(m).seqNam(3); 
                disp(m);

      end
      if (length(struKm(m).seqNam) == 5)
       resultsk.BS{m} = cellstr(struKm(m).seqNam([3,5]));
        %tempcell = struKm(m).seqNam([3,5]); resultsk.BS{m} = cellstr(tempcell);
          disp(m);
      end

end

and the result for this code:

>> resultsk.BS{:}

ans = 

      'CAGCTG'    'CAGGTG'

ans = 

      'CAACTG'

ans = 

      'CAACTG'

The problem with some cells that have two binding sites which made the cell next to cell.

I need them all in one row. still struggling with this. Can you please help?

Thank you, A

[Azzi Abdelmalek]

post a sample of your data

[Abdulaziz]

>AF051909 |392-397:CAGCTG| |413-418:CAGGTG|
tgccgctcagaaaaaaacgatctttggtgaacagtaggagccatctgagcggtgcgacgcattgtgctcccattccacacgctgcggcggccctCAGCTGtcatgcctggaaCAGGTGgtgtaaggcaatccctgggcagccgtgctccccgcccccccccgggccgaccttaaaggcgctgcgtgtgccctggctcctc
>M13483 |445-450:CAACTG|
ccttacatggtctgggggctccctggctgatcctctcccctgcccttggctccatgaatggcctcggcagtcctagcgggtgcgaaggggaccaaataaggcaaggtggcagaccgggccccccacccctgcccccggctgctcCAACTGaccctgtccatcagcgttctataaagcggccctcctggagccagccaccc
>M26773 |446-451:CAACTG|
cttacatggtctgggagccccctggctgatcctctaccctgcccttggctccaagaatggcctcagcggtcctagatggtgctaaggcgaccaaataaggcaaggtggcagatcaggggccccccacccctgcccccggctgctcCAACTGaccccgtccatcagagagctataaagctgcgctccaggcgactgacacc
>M86232 |447-452:CACTTG|
ctgtgctattctggtttggatgtgactcagaacacagttgaacattatttgaactcacagagcttgccattctggaagcacagccttatatgtagtgtccatgggcagtcctattatgggaaagcaacttgagagaaaaggcgggtCACTTGcttgtgcgcaggtcctggaatttgaaatatccagaggcctctacagaa
>M86233 |447-452:CACTTG|
ctgtgctattctagtttggatgtgactcaggacagagttgaacattatttgaattcacagagcttgccatgctggaagcacagccttatatgtagtgtccatgggcagtcctattatggcaaagcaacttgagagaaaaggcgggtCACTTGcttgtgcgcaggtcctggaatttgaaatatccagaggccctacagaat
>X00371 |326-331:CACCTG|
gagctgtcctgcctcgccacaatggCACCTGccctaaaatagcttcccatgtgagggctagagaaaggaaaagattagaccctccctggatgagagagagaaagtgaaggagggcaggggagggggacagcgagccattgagcgatctttgtcaagcatcccagaaggtataaaaacgcccttgggaccaggcagcctca
>X53154 |440-445:CAGCTG|
cgaaggattggtaggcttgccgtcacaggacccccgctggctgactcaggggcgcaggctcttgcgggggagctggcctcccgcccccacggccacgggccctttcctggcaggacagcgggatcttgCAGCTGtcaggggaggggatgacgggggactgatgtcaggaggggatacaaatagtgccgacggctaggggg
>X59034 |442-447:CAGCTG| |461-466:CAGGTG|
accaaacacaatgacaagcctctgactcatgatctatgtagactctcagacactttacatctagtaagagtatagcgatcatgttaagcaaggcacgtctgtggccacagaaggccccaagctttgaggctgtgggcagctCAGCTGtcatgcgggcacaCAGGTGatgtaagacaatagctgtggagtcagctggcttc