!/bin/sh

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 
  
root=~/novell/home/Bioinfo/treball
seq_dir=~/novell/home/Bioinfo/treball/seq-sps2
res_dir=~/novell/home/Bioinfo/treball/blasts-sps2

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 {
	blastdb=`grep "$genome" /cursos/BI/genomes/protists/genomes_list_and_info.tab | cut -f 4`

	for family in `ls $seq_dir`;
	do {
	
                mkdir -p "$res_dir/$family"
                for species in `ls $seq_dir/$family`;
		do {

               query="$seq_dir/$family/$species"
               res_file="$res_dir/$family/tblastn_$species-vs-$genome.fa"
		blastall -p tblastn -i $query -d $blastdb -o $res_file 
                   }
                     done
	}
	done
}
done