I would like to achieve the following things:
Given file contains a job list which I need to execute one by one in a remote server using SSH APIs and store results.
When I try to call the following command directly on remote server using putty it executes successfully but when I try to execute it through python SSH programming it says cant find autosys.ksh.
autosys.ksh autorep -J JOB_NAME
Any ideas? Please help. Thanks in advance.
After reading your comment on the first answer, you might want to create a bash script with bash path as the interpreter line and then the  autosys commands.
This will create a bash shell and run the commands from the script in the shell.
Again, if you are using autosys commands in the shell you better set autosys environment up for the user before running any autosys commands.
How to call .ksh file as part of Unix command through ssh in Python