#!/usr/bin/perl -w

use strict;
use warnings;

#El programa en perl ha estat elaborat per: Laura Cañadas, Clara "Alex" Farrés, Ariadna Pinar, Ana Portillo.



#GENEWISE

print "Proteina:";
my $proteina = <STDIN>;
chomp ($proteina);

print “Scaffold:”;
my $scaffold = <STDIN>;
chomp ($scaffold);

system (“genewise -pep -pretty -cdna -gff $proteina $proteina.$scaffold.fastasubseq.fa.sed”);

system (“emacs genewise.fa”);

system (“t_coffee genewise.fa $proteina > wisecoffee.txt”);

print “s’ha fet el t-coffee”;