#!/bin/bash

module load python

TD_OUT=TranD_mel2mel_map_check
    mkdir -p ${TD_OUT}

python add_prefix_gtf.py \
    -g mel2mel_corrected_associated_gene.gtf \
    -t transcript_id \
    -p map \
    -o ${TD_OUT}/mel2mel_map_prefix.gtf

cat dmel-all-r6.17.gtf ${TD_OUT}/mel2mel_map_prefix.gtf \
    > ${TD_OUT}/mel2mel_map_check.gtf

python id_ujc.py \
    --gtf mel2mel_map_check.gtf \
    -x mel \
    --skip-gtf \
    -o ${TD_OUT} \
    -p mel2mel_ref


TD_OUT=TranD_sim2sim_map_check
    mkdir -p ${TD_OUT}

python add_prefix_gtf.py \
    -g sim2sim_corrected_associated_gene.gtf \
    -t transcript_id \
    -p map \
    -o ${TD_OUT}/sim2sim_map_prefix.gtf

cat dsim-all-r2.02.gtf ${TD_OUT}/sim2sim__map_prefix.gtf \
    > ${TD_OUT}/sim2sim__map_check.gtf

python id_ujc.py \
    --gtf sim2sim_map_check.gtf \
    --skip-gtf \
     -x sim \
    -o ${TD_OUT} \
    -p sim2sim_ref