matlab script to run a perl script in a loop

Dear all, I have a perl script that I need to run 2000 times.

myscript.pl -w i -f A1simple.fa >A1_i .fa.real. j .out

where i=3:20 and j=100.

The perl script works well for a single run, ie:

   myscript.pl -w 3 -f A1simple.fa >A1_3.fa.real.1.out

However, I didn't find a way to run it in a loop.

The loop should look something like this:

for i=20:-1:3
  for j=1:100
perl ('myscript.pl -w', i, '-f A1simple.fa >A1_', i, '.fa.real.', j, '.out')
  end
end

Thanks in advance.

Diego

Answer 1

[Walter Roberson]

perl( sprintf('myscript.pl -w %d -f A1simple.fa >A1_%d.fa.real.%d.out', i, i, j) )

[Diego]

Happy new year Walter!

Many thanks!

Diego

[Diego]

Dear Walter,

I'm sorry but that didn't work.

I receive the following errors:

Error using perl (line 45)

Unable to find Perl file: myscript.pl -w 3 -f A1simple.fa >A1_3.fa.real.1.out

Error in myscript (line 4)

perl( sprintf('myscript.pl -w %d -f A1simple.fa >A1_%d.fa.real.%d.out', i, i, j) )

[Diego]

I created a long script using MSAccess, so that solved my problem.

Still I'm curious about the way of doing this with a few lines inside Matlab.

Regards,

Diego

[Walter Roberson]

Somehow I'm not really surprised. You could take the sprintf() result and do a split on it at whitespace to create a cell array of strings, and then you could perl(TheCellArray{:})

However, I have my doubts as to whether perl itself supports the I/O redirection operator. I think you would be better off passing the output file name to the script and having the script open the file for writing. Pass the file name as the first argument and shift() before you use <> the first time.

[Diego]

Thank you Walter.

I will try that in short.

Best,

Diego