Question

Hey so I have a bash command that echos a string based on reading some file. Say for simplicity it is like this

for line in `cat file`
do
if [ "$line" == "IwantThisLine" ]
then   
echo "True"
fi
done

And I have it saved as its own individual script. Its called readRef.sh. So now I want to call it in matlab and store whatever it outputs in a variable! I am not entirely sure on how to do that, I seem to get an error when using evalc() on a system(). But it could be just me messing up quotations.

I tried something like

evalc(system(['./readRef.sh ' bamfile']))

The “bamfile” is a variable that is just a string to the path of a bamfile.

I get this error.

>> tes = evalc(system(['./readRef.sh ' smplBamFile])) 
hg18 
??? Undefined function or method 'evalc' for input arguments of type 'double'.

Coincidentally it does spit out “hg18” which is what I want to set the matlab variable to be.

Answer 1

Oh, I see. I don’t think you need evalc at all. Reading the system docs you can just do:

[status, result] = system('echo True; echo "I got a loverly bunch of coconuts"')

And result will be

True
I got a loverly bunch of coconuts

So just do:

 [status, result] = system(['./readRef.sh ' smplBamFile])

The reason evalc isn’t working is that it requires its input to be a Matlab expression in a string, but you are passing it the result of system.

You could try:

 evalc("system(['./readRef.sh ' smplBamFile])")

See how I’m passing in the system(...) as a string?