#!/usr/bin/perl -w
use strict;

my $q; #query
my $genome; #fasta organism sequence

#First the program asks for the name of the protein we want to work with, in order to name the files and to know which query to take

print "Enter the query name:\n";
$q = <STDIN>;
chomp ($q);

print "Running blast \n";

system ("tblastn -query $q -db /cursos/20428/BI/genomes/2017/Pogona_vitticeps/genome.fa -outfmt 7 -out $q.blast");

print "Blast ended \n";

#The program shows us the result from blast in the screen so we can choose which hits to analyze

system ("more $q.blast");

print "\n";

print "Next steps:\n";

#Finally the program opens the second program, that will perform the rest of the analysis

system ("perl programa.pl"); 
