#!/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
../7.Misc/illegal_filter.py ${infa} > tmp
cat tmp | awk '{print $1}' > tmp.fa
../7.Misc/subset_fasta.py tmp.fa -l 200 -n 5000 --row_len 0 -o ${outfile}.fa
rm tmp.fa
rm tmp
transeq -frame F ${outfile}.fa ${outfile}.p.fa
cat ${outfile}.fa | grep ">" | cut -d '>' -f2  >${outfile}.txt
cat ${ingtf} |cgat gtf2gtf -m filter --filter-method=transcript --map-tsv-file=${outfile}.txt |grep -v "#" > tmp.gtf
../7.Misc/gtf2COME.py tmp.gtf > ${outfile}.gtf
rm tmp.gtf