#!/bin/bash
source moduls;
##read -p "Introdueix la PROTeina:" PROT;
#mkdir $PROT

#cd ~/Ammotragus/
prot_list=$(echo "$(for i in  */*exone*; do if [ $(more $i|grep -c "# --- END OF GFF DUMP ---") -gt 1 ]; then echo $i|grep -v gff; fi; done)"|sed 's/.exonerate.*//g')

#read -r -a prot_ar <<< """$prot_list"""

prot_ar=()
while read -r line; do
   prot_ar+=("$line")
done <<< "$prot_list"

for index in "${!prot_ar[@]}"
do
#echo $prot_ar

PROT=$(echo "${prot_ar[index]}"|sed 's/\/.*//')
contig=$(echo "${prot_ar[index]}"|sed 's/.*-//')

originfa=$(find $PROT-*)
echo $originfa

echo $PROT-$contig



cd $PROT

#fastasubseq -f $contig.fetch -s $origin -l $length > $PROT-$contig.subseq;
#head $PROT-$contig.subseq                                                      

exonerate -m p2g --showtargetgff -q ../$originfa -t $PROT-$contig.subseq -n 1 > $PROT-$contig.exonerate1
#exonerate --exhaustive yes -m p2g --showtargetgff -q ../$originfa -t $PROT-$contig.subseq > $PROT-$contig.exonerate
#head $PROT-$contig.exonerate                                                   

egrep -w exon $PROT-$contig.exonerate1 > $PROT-$contig.exonerate.gff;
#head $PROT-$contig.exonerate.gff

fastaseqfromGFF.pl $PROT-$contig.subseq $PROT-$contig.exonerate.gff > $PROT-$co\
ntig.nt.fa;
#head $PROT-$contig.nt.fa                                                       

fastatranslate -f $PROT-$contig.nt.fa -F 1 > $PROT-$contig.prot;
sed -i -e'/^>/! s/*/X/g' $PROT-$contig.prot
#head $PROT-$contig.prot                                                        

t_coffee $PROT-$contig.prot ../$originfa > $PROT-$contig.tcoffee_exo 2>../\
tcoffe_trash;
#head $PROT-$contig.tcoffee;                                                    

#genewise -pep -pretty -cdna -gff -both ../$originfa $PROT\
#-$contig.subseq >$PROT-$contig.gen;

#t_coffee $PROT-$contig.prot1 ../$originfa > $PROT-$contig.tcoffee_gen 2>../\
#tcoffe_trash;
#head $PROT-$contig.tcoffee;                                                    

cd ..

#done 
done