#!/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

exonerate -m p2g --showtargetgff -q /home/u49707.est12.alu.upf/novell/home/bioinfo/TREBALL/querysU/u_${query}.fa -t /home/u49707.est12.alu.upf/novell/home/bioinfo/TREBALL/hits/fastasubseq/$x --exhaustive yes > ./direxonerate/alineament_${hit}_$genoma.gff

exonerate -m p2g --showtargetgff -q /home/u49707.est12.alu.upf/novell/home/bioinfo/TREBALL/querysU/u_${query}.fa -t /home/u49707.est12.alu.upf/novell/home/bioinfo/TREBALL/hits/fastasubseq/$x --exhaustive yes | egrep -w exon > ./direxonerate/alineament_$x.exonerate.gff

fastaseqfromGFF.pl /home/u49707.est12.alu.upf/novell/home/bioinfo/TREBALL/hits/fastasubseq/$x ./direxonerate/alineament_$x.exonerate.gff > cDNA_$x

fastatranslate ./cDNA/$x > ./transcrits/transcrits_${hit}_$genoma.fa

} done