#!/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

mkdir genewise genewise_complet

for genome in Crithidia_fasciculata Trypanosoma_congolense Leishmania_tarentolae Leishmania_donovani_BPK282A1 Ichthyophthirius_multifiliis_strain_G5 Phytophthora_capsici Sphaeroforma_arctica Fragilariopsis_cylindrus Dictyostelium_fasciculatum Dictyostelium_discoideum_AX4 Albugo_laibachii_Nc14; do {

for seq in selprotT_human.fa selprotT_mouse.fa selR1_human.fa selR2_human.fa selR3_human.fa selR_cerevisiae.fa selR_droso.fa selR_elegans.fa; do {

# La comanda '-both' nos permite obtener la predicción de la proteína forward y reverse.

genewise -pep -both $seq subseq/subseq.${seq}.CONTRA.${genome}.fa > genewise/genewise_${seq}.CONTRA.${genome}.fa

genewise -pep -cDNA -pretty -both -gff $seq subseq/subseq.${seq}.CONTRA.${genome}.fa > genewise_complet/genewise_${seq}.CONTRA.${genome}.fa

} done

} done