#!/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.


print "Introdueix nom de la proteina del genoma de referència:";
my $proteina = <STDIN>;
chomp ($proteina);



# FASTAFETCH

print "Introdueix el nom del scaffold:";
my $scaffold = <STDIN>;
chomp ($scaffold);

system ("mkdir $proteina.$scaffold"); # creem carpeta amb el nom del scaffold triat

system ("fastafetch /cursos/20428/BI/genomes/2017/Sporophila_hypoxantha/genome.fa /cursos/20428/BI/genomes/2017/Sporophila_hypoxantha/genome.index $scaffold > $proteina.$scaffold.fastafetch.fa");
 
print "Fastafetch completat\n\n";



# FASTASUBSEQ

print "Start:";
my $start = <STDIN>;
chomp ($start);

$start = $start - 50000;
print "L'inici és $start\n";

if ($start < 0) { 	
    $start = 1; 	# Fem que comenci per 1
}

print "Final:";
my $final = <STDIN>;
chomp ($final);

$final = $final + 50000;

print "El final és $final\n";

#Fem un fastalength per saber la llargada del scaffold

system ("fastalength $proteina.$scaffold.fastafetch.fa");

print "Aquesta es la llargada del scaffold\n";

print "Assegura't que els límits es troben dins la llargada del scaffold\n"; 

print "Introdueix la llargada del scaffold:";

my $lsca= <STDIN>; #Introduim l'output del fastalenght

if($lsca > $final){
    print "Apreta enter per continuar";
    <>;
}
else{
	$final = $lsca;
	chomp ($final);
	print "la posició final es $final\n";
}

my $lenght = $final - $start;

system ("fastasubseq $proteina.$scaffold.fastafetch.fa $start $lenght > $proteina.$scaffold.fastasubseq.fa");

print "Fastasubseq fet\n";



# EXONERATE 

system ("exonerate -m p2g --showtargetgff -q $proteina -t $proteina.$scaffold.fastasubseq.fa --exhaustive yes > $proteina.$scaffold.exon.gff");

system ("emacs $proteina.$scaffold.exon.gff");

system ("egrep -w exon $proteina.$scaffold.exon.gff > $proteina.$scaffold.egrep.gff");

print "Exonerate fet\n";



# FASTASEQFROMGFF

system ("fastaseqfromGFF.pl $proteina.$scaffold.fastasubseq.fa  $proteina.$scaffold.egrep.gff > $proteina.$scaffold.nt.fa");

print "Fastasqfromgff fet\n";



# FASTATRANSLATE 

system ("fastatranslate -f $proteina.$scaffold.nt.fa -F 1 > $proteina.$scaffold.pep.fa");

print "Fastatranslate fet\n";



# TCOFFEE  

system ("t_coffee $proteina.$scaffold.pep.fa $proteina > $proteina.$scaffold.final.txt");

print "Tcoffee fet\n\n";



#Sed

system ("cp $proteina.$scaffold.fastasubseq.fa $proteina.$scaffold.fastasubseq.fa.sed");
system ("sed -i 's/Y/N/g' $proteina.$scaffold.fastasubseq.fa.sed");
system ("sed -i 's/M/N/g' $proteina.$scaffold.fastasubseq.fa.sed");
system ("sed -i 's/W/N/g' $proteina.$scaffold.fastasubseq.fa.sed");
system ("sed -i 's/R/N/g' $proteina.$scaffold.fastasubseq.fa.sed");
system ("sed -i 's/S/N/g' $proteina.$scaffold.fastasubseq.fa.sed");
system ("sed -i 's/K/N/g' $proteina.$scaffold.fastasubseq.fa.sed");

print "S’ha fet el sed a l’arxiu fastasubseq.fa\n";



system ("mv $proteina.$scaffold.fastafetch.fa $proteina.$scaffold");
system ("mv $proteina.$scaffold.fastasubseq.fa $proteina.$scaffold");
system ("mv $proteina.$scaffold.exon.gff $proteina.$scaffold");
system ("mv $proteina.$scaffold.egrep.gff $proteina.$scaffold");
system ("mv $proteina.$scaffold.nt.fa $proteina.$scaffold");            
system ("mv $proteina.$scaffold.pep.fa $proteina.$scaffold");
system ("mv $proteina.$scaffold.final.txt $proteina.$scaffold");
system ("mv $proteina.$scaffold.pep.aln $proteina.$scaffold");
system ("mv $proteina.$scaffold.pep.html $proteina.$scaffold");
system ("mv $proteina.$scaffold.fastasubseq.fa.sed $proteina.$scaffold");
system ("cp $proteina $proteina.$scaffold");

print "S'han passat tots els fitxers a la carpeta $proteina.$scaffold\n";