#!/usr/bin/env sh

help="[Usage] ./prepare_data.sh infasta ingtf outfileprefix"
infa=$1
ingtf=$2
outfile=$3
if [[ $# -eq 0 ]];then
    echo ${help}
    exit 2
fi
subset_fasta.py ${infa} -l 200 -n 5000 -o ${outfile}.fa
cat ${outfile}.fa | awk -F "|" '{print$1}'> tmp
../7.Misc/illegal_filter.py tmp > tmp.fa
mv tmp.fa ${outfile}.fa
rm tmp
transeq -frame F ${outfile}.fa ${outfile}.p.fa
cat ${outfile}.fa | grep ">" | cut -d '>' -f2 | cut -d '|' -f1 >${outfile}.txt
cat ${ingtf} |cgat gtf2gtf -m filter --filter-method=transcript --map-tsv-file=${outfile}.txt |grep -v "#" > ${outfile}.gtf
if [[ ${species} == "human" ]];then
    ../7.Misc/gtf38to19.sh ${outfile}.gtf ${outfile}_hg19.gtf
fi