How to execute commands from a Ubuntu executable in php?

Question

run in Ubuntu the following line:

needle alvo.txt modelo.txt

when running it displays these lines:

Needleman-Wunsch global alignment of two sequences

I need to enter to go as default in this:

Gap opening penalty [10.0]:

and in that:

Gap extension penalty [0.5]:

and one more enter to have the final file on that line :

Output alignment [hba_human.needle]:

how to put these commands to be executed in php code?

tried running the command shell_exec ('needle alvo.txt modelo.txt') the problem is that the program is not an executable of a line need to give the Enters to go as default the other lines.

Answer 1

You can write a script in expect and call it from your PHP code. Example:

#!/usr/bin/expect

set timeout 10
set alvo [lindex $argv 0]
set modelo [lindex $argv 1]

spawn ./needle $alvo $modelo
expect "Gap opening"    {send "\r"}
expect "Gap extension"  {send "\r"}
expect "Gap alignment"  {send "\r"}

This script basically runs your command line and waits for "Gap..." returns to send "Enter".