#!/bin/bash 

rm resultats_exonerate.txt 2> error.temp 

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 

adresa="/cursos/BI/genomes/protists/2012" 

mkdir regions
mkdir subseq
mkdir exonerate_output
mkdir exons
mkdir cDNA
mkdir translations
mkdir translationsok
mkdir genewise

for proteins in blast_selec/* ; do { 
       for genome in $proteins/*; do { 
               for hit in $genome/* ; do { 

		### Assignem a les variables els noms sense rutes ni extensions 
		 
		proteins=`basename $proteins` 
        		genome=`basename $genome` 
        		hit=`basename $hit` 
		hit=${hit%.txt}	 

		echo ${proteins}_${genome}_${hit}: 

		### Per emmagatzemar la regio; on apareix el hit 

		regio=`cat ./blast_selec/$proteins/$genome/$hit.txt | cut -f 2` 
		fastafetch $adresa/$genome/genome.fa ./llibreria/genomes/$genome.index $regio > ./regions/$regio.fa 
		 
		### Aqui; definim l'inici i el final del hit en la regio

		inici=`cat ./blast_selec/$proteins/$genome/$hit.txt | cut -f 9` 
		final=`cat ./blast_selec/$proteins/$genome/$hit.txt | cut -f 10` 

		if [ "$inici" -gt "$final" ]; then 
			inici="$final" 
		fi 

		start=$(expr $inici - 15000 ) 
		length="50000" 


		### FASTASUBSEQ: Retalla una regio; al voltant del gen que volem fer servir	 

		fastasubseq ./regions/$regio.fa $start $length > ./subseq/${proteins}_${genome}_${hit}_genomic.fa 2> error_msg.temp 


		### Aixo; ens servira per modificar variables en cas que no hi hagi prou bases en la regio o que l'inici estigui massa aprop 
					 
		error=`cat error_msg.temp` 
		if [ "$error" != "" ]; then 
			error_llarg=`cat error_msg.temp | egrep "before end"` 
			error_curt=`cat error_msg.temp | egrep "Unknown flag"` 
						 
			### Si es passa de llarg, establim la llargada perque arribi al final 
			if [ "$error_llarg" != "" ]; then 
				llargada=$error_llarg						 
				llargada=${llargada##*(} 
				llargada=${llargada%)} 
				length=$(( $llargada - $start)) 
				fastasubseq ./regions/$regio.fa $start $length > ./subseq/${proteins}_${genome}_${hit}_genomic.fa 
			fi 
						 
			### Si l'inici esta massa aprop establim l'start en 0 
			if [ "$error_curt" != "" ]; then 
				start="0" 
				fastasubseq ./regions/$regio.fa $start $length > ./subseq/${proteins}_${genome}_${hit}_genomic.fa 2> error_msg_2.temp 
				error_2=`cat error_msg_2.temp` 
				if [ "$error_2" != "" ]; then 
					error_2_llarg=`cat error_msg_2.temp | egrep "before end"` 
					if [ "$error_2_llarg" != "" ]; then 
						llargada=$error_2_llarg						 
						llargada=${llargada##*(} 
						llargada=${llargada%)} 
						length=$(( $llargada - $start)) 
						fastasubseq ./regions/$regio.fa $start $length > ./subseq/${proteins}_${genome}_${hit}_genomic.fa 2> error_msg_3.temp 
					fi 
				fi 
			fi 
		fi 


		### EXONERATE : Prediccio de gens 
		 
		echo "Iniciant exonerate" 

		exonerate -m p2g --showtargetgff -q ./llibreria/$proteins -t ./subseq/${proteins}_${genome}_${hit}_genomic.fa > ./exonerate_output/exonerate_${proteins}_${genome}_${hit}.gff 2> error_de_substitucio.temp 

echo "Exonerate acabat!" 

		### Per extreure els exons				 
		 
		echo "Preparant i executant extreure exons" 
				 
		exon=`grep -w exon ./exonerate_output/exonerate_${proteins}_${genome}_${hit}.gff` 
		grep -w exon ./exonerate_output/exonerate_${proteins}_${genome}_${hit}.gff > ./exons/exon_${proteins}_${genome}_${hit}.gff 

	 
echo ${proteins}_${genome}_${hit} fet 

		
		### Per traduir el cDNA 

		echo 'Traduint a cDNA'

		fastaseqfromGFF.pl ./subseq/${proteins}_${genome}_${hit}_genomic.fa ./exons/exon_${proteins}_${genome}_${hit}.gff > ./cDNA/cDNA_${proteins}_${genome}_${hit}.fa 
		fastatranslate ./cDNA/cDNA_${proteins}_${genome}_${hit}.fa > ./translations/aa_${proteins}_${genome}_${hit}.fa 
	 
echo ${proteins}_${genome}_${hit} fet 


		## Per escollir el frame 1 si i nomes si es l'optim 
		fastatranslate ./cDNA/cDNA_${proteins}_${genome}_${hit}.fa -F 1 > ./translationsok/aa_${proteins}_${genome}_${hit}.fa 

		### Pel Genewise 
		echo 'Començant Genewise'
		 
		genewise -pep -pretty -cdna -gff ./llibreria/$proteins ./subseq/${proteins}_${genome}_${hit}_genomic.fa > genewise/genewise_${proteins}_${genome}_${hit}.txt 


		} done 
	} done 
} done 

rm *.temp