Run Unafold Melting.Pl From Matlab

Question

[Mike]

Hello,

i'm have been trying to get matlab run the UNAFold melt.pl pearl script and to retrieve the results.

But i'm stuck right now.

One approach was to generate a batch-file with the syntax, but this did not worked out:

UNAFoldDir = 'C:\UNAFold\bin\';

Seq1Name = 'Seq1'; Seq1Sequence = 'CTGCTTTCCTGAGAGCAGTACCTCATTAGTTTCCCTGAATTTGGGGGGGGGGG'; Seq1 = struct('Header', Seq1Name, 'Sequence', Seq1Sequence); fastawrite(strcat(UNAFoldDir, 'Seq1.fas'), Seq1);

% Write StartUNA File fid = fopen(strcat(UNAFoldDir, 'StartUNA.bat'),'w'); fwrite(fid, ['perl ..\bin\melt.pl -n DNA -C 0.1 Seq1.fas Seq1.fas > Seq1-Seq2-Results.txt']); fclose(fid);

Then i tryed it with the Matlab in-build pearl commando:

perl('C:\UNAFold\bin\melt.pl','-n DNA -C 0.1 Seq1.fas Seq1.fas')

But all i get are error messages like this one: ??? Error using ==> perl at 82 System error: Error: file not specified Run 'melt.pl -h' for help Command executed: perl C:\UNAFold\bin\melt.pl "-n DNA -C 0.1 C:\UNAFold\bin\Seq1.fas C:\UNAFold\bin\Seq1.fas"

Running perl('C:\UNAFold\bin\melt.pl','-h') works fine, so there should be no problem with the directory-path from unafold.

I have never worked with UNAFold/Pearl-scripts before.

I would be grateful for every suggestion! :-)

Best regards, Mike

[Eric Fournier]

Does the file "C:UNAFoldbinSeq1.fas" exist? If so, are you sure melt.pl does not require any other files to be specified on the command line?

Answer 1

[Mike]

Hello Lars,

i found an solution, there was only a mistake in the syntax (on both sides, perl- & matlab-code):

perl('C:UNAFoldbinmelt.pl', '-n', 'DNA', '-C', '0.01', 'Seq1.fas', 'Seq1.fas)

works now, and it does not need a batch file to work so no "painful" data in via matlab and some files generated by unafold. ;-)

br, mike