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Also, imagine MyProgram1 contains the following (do not forget the ';' between the commands):

#!/bin/bash
echo 'print 2+2'
sleep 4
echo ';'
echo 'print "toto"'

You can do, for example:

 sage -c $(./MyProgram1) | sed 's/4/5/g' > final_output

and get, in final_output:

5
toto