Question

I am trying to retrieve particular data from a txt file and would like to save it in a new txt file.

Here’s the sample of the data that i would like to retrive from the text file:

//
FORMAT CDDF1.0
DOMAIN 1cuk003
VERSION   3.1.0
VERDATE   20-Jan-2007
NAME   Ruva protein. Chain: null. Engineered: yes
SOURCE Escherichia coli. Strain: 12 bl21 (de3).  Expressed in: escherichia co
SOURCE li.
CATHCODE  1.10.8.10
CLASS  Mainly Alpha
ARCH   Orthogonal Bundle
TOPOL  Helicase, Ruva Protein; domain 3 
HOMOL  DNA helicase RuvA subunit, C-terminal domain
DLENGTH   48
DSEQH  >pdb|1cuk003
DSEQS  TDDAEQEAVARLVALGYKPQEASRMVSKIARPDASSETLIREALRAAL
NSEGMENTS 1
SEGMENT   1cuk003:1:1
SRANGE START=156  STOP=203
SLENGTH   48
SSEQH  >pdb|1cuk003:1:1
SSEQS  TDDAEQEAVARLVALGYKPQEASRMVSKIARPDASSETLIREALRAAL
ENDSEG
//

From those details, I am trying to retrieve “DOMAIN, SRANGE START AND STOP”, but i would just like to select the information, not the header of the file name. For an example, DOMAIN is 1cuk003, i would just like to select “1cuk003” from it.

Do i need to store this data in an array? Or is there any other way that i could use to solve this problem. Also, i have over 10,000 entrires more of this data with different values.

The other part is that, once i have retrived those data, i would then like to format the data using “sprintf”, eg. sprintf('INSERT INTO postgres VALUES %d,%d.',array1,array2);

Is this possible?

Basically, in the end, I would like to have a text file, containing SQL INSERT statements of all the data been stored in which i can just easily execute them in PostgreSQL.

I did a test code in which it opens a text file, replicates the data and saves it in a new text file.

fid = fopen('sample.txt');    
readfile = fread(fid, '*char');    
fclose(fid);                        
output = fopen('output_sample.txt', 'wt');
fprintf(output,'%s \n', readfile);
fclose(output);

Thank you.

Answer 1

There are several MATLAB functions which come in handy:

• fgetl: Read a single line from a file
• strtok: Split a string
• switch: Choose from different actions
• regexp: Match regular expressions

Armed with these, the basic workflow is like that:

domain = '';
start = '';
stop = '';
fin = fopen('sample.txt', 'r');
fout = fopen('output.txt', 'w');
% TODO: Add error check!
while true
    line = fgetl(fin); % Get the next line from the file
    if ~ischar(line)
        % End of file
        break;
    end
    [key, value] = strtok(line); % Split line at the first space
    switch key
        case 'DOMAIN'
           % Store domain
           domain = value;
        case 'SRANGE'
           % Retrieve start and stop values
           m = regexp(value, 'START=(\d+)\s*STOP=(\d+)', 'tokens');
           start = m{1};
           stop = m{2};

           % Print result
           fprintf(fout, 'INSERT INTO postgres VALUES %s, %s, %s.\n', domain, start, stop);
    end
end
fclose(fin);
fclose(fout);

I currently do not have access to a MATLAB installation, so the code above is not tested. It should get you going, though.