Running .exe with system()

Hi everybody!

I'm trying to run RNAfold.exe with the matlab system command.The command line call is as follows:

RNAfold -p -d2 --noLP -P dna_mathews.par --noconv < sequence1.fa > sequence1.out

I tried to obtain the same in matlab using the following code:

[status, result]=system(['RNAfold.exe  <', 'sequence1.txt'], '-echo');

It works but only partially. I can input the system with the correct file but not the specified options such as for example the parameters that should be used (e.g. dna_mathews.par).

I would like to know if it's possible to only input the file but also the options. Can anyone help me with this?

Thanks in advance!

Iene

[Fangjun Jiang]

Did you try the whole string that is used in Command line

system('RNAfold -p -d2 --noLP -P dna_mathews.par --noconv < sequence1.fa > sequence1.out')

[Iene Rutten]

Thank you for you answer but unfortunately yes and the error is:

Error using system
Unrecognized option: -p -d2 --noLP -P dna_mathews.par --noconv < sequence1.fa > sequence1.out

Answer 1

[Fangjun Jiang]

Try this:

1. Put this line into a text file called input.txt

-p -d2 --noLP -P dna_mathews.par --noconv < sequence1.fa > sequence1.out

2. Run this in MATLAB

system('RNAfold < input.txt')