#!/bin/bash

interruptor="0"

rm resultats.txt 2> error.txt

for query in sel1human sel1mus sel1tn; do {

for genome in  A.taiwanensis B.hominis C.merolae C.muris C.owczarzaki C.parvum E.siliculosus H.arabidopsidis N.gruberi P.pallidum P.tricornutum P.ultimum S.parasitica T.trahens; do {
	if [ "$interruptor" = "0" ]; then
		mkdir ./blast/$genome 2> error.txt
	fi
          blastdb=`grep $genome /cursos/BI/genomes/protists/genomes_list_and_info.tab | cut -f 4`
          blastall -p tblastn -d $blastdb -i ./$query.txt -o ./blast/$genome/${genome}_$query.txt -m 9 2> error.txt
	echo ${query}_$genome : >> resultats.txt
	egrep SPP ./blast/$genome/${genome}_$query.txt | egrep e- >> resultats.txt
	egrep SPP ./blast/$genome/${genome}_$query.txt | egrep e- > temp
	./substitucio.pl < $query.txt > posicio.txt
	echo ${query}_$genome : >> resultats_$query.txt
	./filtre_U.pl < temp >> resultats_$query.txt
	  echo ${query}_$genome fet

        } done
interruptor="1"
} done