#!/bin/bash 

export PATH=/cursos/BI/bin/ncbiblast/bin:$PATH 
cp /cursos/BI/bin/ncbiblast/.ncbirc ~/ 
export PATH=/cursos/BI/bin/exonerate/i386/bin:$PATH 
export PATH=/cursos/BI/bin:$PATH 
export WISECONFIGDIR=/cursos/BI/soft/wise-2.2.0/wisecfg 

adresa="cursos/BI/genomes/protists/2012" 

    
    for proteines_fa in ./llibreria/*.fa; do { 
	basename_fa=`basename $proteines_fa` 
	proteines=$proteines" $basename_fa" 
 } done 

rm resultats_blast.txt 2> error.temp 

    for protein in $proteines ; do { 

	for genomes in A.laibachii_Nc14 A.rara C.fasciculata D.discoideum_AX4 D.fasciculatum F.cylindrus G.niphandrodes I.multifiliis_strain_G5 L.donovani_BPK282A1 L.tarentolae P.capsici P.polycephalum S.arctica T.congolense; do { 
patroalfa=`cat ./llibreria/$protein | egrep ^">"` 
patrobeta=${patroalfa#*>} 
			echo $patrobeta > temppatro 
			patro=`cut -f 1 -d " " temppatro` 
			rm temppatro 

blastall -p tblastn -i ./llibreria/$protein -d /cursos/BI/genomes/protists/2012/$genomes/genome.fa -o ./llibreria/genomes/output_blast/$protein.$genomes.txt -m 9 -e 0.001 
			echo ">${protein}_$genomes:" >> resultats_blast.txt 
			egrep $patro ./llibreria/genomes/output_blast/$protein.$genomes.txt | egrep e- >> resultats_blast.txt 


x=`egrep $patro ./llibreria/genomes/output_blast/$protein.$genomes.txt | egrep e-` 
               

			if [ "$x" != "" ]; then 
				egrep $patro ./llibreria/genomes/output_blast/$protein.$genomes.txt | egrep e- > arxiu.temp 

				mkdir -p ./blast_selec/$protein 2> error.temp 
				mkdir -p ./blast_selec/$protein/$genomes 2> error.temp 
				./llibreria/dosificador.pl $protein $genomes < arxiu.temp 
                                rm -f error.temp arxiu.temp 

			fi 
echo ${protein}_$genomes fet 
		} done 
	} done 
rm -f ./*.temp