#!/bin/bash

for arxiu in /home/u49707.est12.alu.upf/novell/home/bioinfo/TREBALL/hits/fastasubseq/* ; do {

x=`basename $arxiu`
query=${x#*_}
query=${query%_*}
query=${query#*_}

genoma=${x##*_}
genoma=${genoma%_*}
genoma=${genoma%.fa}

hit=${x#*_}
hit=${hit%_*}

echo x $x

#./canviU.pl < ./query/$query.fa > ./querysU/u_${query}.fa

genewise -pep -pretty -cdna -gff ./query/$query.fa ./hits/fastasubseq/$x.fa > gw_fw_${hit}_$genoma

} done