How to do [batch run unblur]

Submitted by yingyizhang on Thu, 2016-05-12 09:21

Forums

Unblur & Summovie

Dear All,

I am running unblur for the stacks.
Is it possible to run it by setting all the input/output/parameters into one single command line instead of typing in the parameters one by one? So that it is easier to run unblur for many stacks.

Thanks so much.

Cheers,
Yingyi

Alexis Thu, 2016-05-12 09:26

Dear Yingyi,

It's not possible to call unblur with a single command line. However, it is trivial to write a script to loop over many stacks. In pseudo-bash syntax, it would look like this:


for stack_filename in stacks/????.mrc; do
unblur.exe <<eof
${stack_filename}
${number_of_frames}
${output_filename}
${shifts_output_filename}
no
${pixel_size}
yes
${exposure_per_frame}
${acceleration_voltage}
0.0
no
no
eof
done

Hope this helps
Alexis