#!/bin/bash
GENOMA="/cursos/BI/genomes/project_2013/Nomascus_leucogenys/genome.fa"

QUERYNAME=$1
SEQNAME=$2
START=$3
END=$4

DIR=$QUERYNAME.$SEQNAME

# Creem la carpeta de resultats per a cada query
mkdir -p $DIR 

echo Procesant $QUERYNAME $SEQNAME $START $END
echo
echo "FASTAFETCH"
fastafetch $GENOMA genome.index $SEQNAME > $DIR/$SEQNAME.fa

let START=START-50000
let LENGTH=(END-START)+50000
echo "FASTASUBSEQ"
fastasubseq $DIR/$SEQNAME.fa $START $LENGTH > $DIR/$SEQNAME.subseq

# Executem exonerate
echo "EXONERATE"
export PATH=/cursos/BI/soft/exonerate/exonerate-2.2.0-i386/bin/:$PATH
exonerate -m p2g --showtargetgff -q $QUERYNAME.fa -t $DIR/$SEQNAME.subseq |grep "cds" > $DIR/$SEQNAME.exonerate

# Executem exonerate sencer
echo "EXONERATE SENCER"
export PATH=/cursos/BI/soft/exonerate/exonerate-2.2.0-i386/bin/:$PATH
exonerate -m p2g --showtargetgff -q $QUERYNAME.fa -t $DIR/$SEQNAME.subseq > $DIR/$SEQNAME.exoneratesencer

# Executem genewise
echo "GENEWISE"
export PATH=/cursos/BI/bin:$PATH
export WISECONFIGDIR=/cursos/BI/soft/wise-2.2.0/wisecfg
genewise -pep -pretty -cdna -gff $QUERYNAME.fa $DIR/$SEQNAME.subseq|grep "cds" > $DIR/$SEQNAME.genewise

# Executem genewise sencer
echo "GENEWISE SENCER"
export PATH=/cursos/BI/bin:$PATH
export WISECONFIGDIR=/cursos/BI/soft/wise-2.2.0/wisecfg
genewise -pep -pretty -cdna -gff $QUERYNAME.fa $DIR/$SEQNAME.subseq > $DIR/$SEQNAME.genewisesencer

# Traduim els exons exonerate
echo "GFF"
fastaseqfromGFF.pl $DIR/$SEQNAME.subseq $DIR/$SEQNAME.exonerate > $DIR/$SEQNAME.cdnaE 
echo "FASTATRANSLATE"
fastatranslate -F 1 $DIR/$SEQNAME.cdnaE > $DIR/$SEQNAME.aaE.fa

# Traduim els exons genewise
echo "GFF2"
fastaseqfromGFF.pl $DIR/$SEQNAME.subseq $DIR/$SEQNAME.genewise > $DIR/$SEQNAME.cdnaG 
echo "FASTATRANSLATE2"
fastatranslate -F 1 $DIR/$SEQNAME.cdnaG > $DIR/$SEQNAME.aaG.fa

# Executem t-coffee de les seqüències exonerate i genewise
export PATH=/cursos/BI/bin:$PATH
echo "TCOFFEE"
t_coffee $QUERYNAME.fa $DIR/$SEQNAME.aaE.fa -outfile $DIR/$SEQNAME.tcoff.E.aln
t_coffee $QUERYNAME.fa $DIR/$SEQNAME.aaG.fa -outfile $DIR/$SEQNAME.tcoff.G.aln

# Executem SECISearch
echo "SECISearch"
SECISearch.pl $DIR/$SEQNAME.subseq > $DIR/$SEQNAME.secis</pre>