RUN_validate_DELS.sh

#!/bin/bash

#input_TP_4=./test_sample/deletions_SAMPLE.csv
input_TP_4=$1

#$2='./test_sample/'
outputf=$2'output_deletions/'
mkdir $outputf
#output_path_TP_4=./test_sample/output_deletions/ 
output_path_TP_4=$outputf
# ________________________________________________________________________________________________
echo "Processing data:"

# look scripts:
python look_repRegions2.py $input_TP_4 $output_path_TP_4 &
python look_segDuplications2.py $input_TP_4 $output_path_TP_4 &

# Segmental Duplcations and Repititve regions covereage:
python segDuplication_coverage.py $input_TP_4 $output_path_TP_4 &

python repRegions_coverage.py $input_TP_4 $output_path_TP_4 &
python segDUPS_find_pair2.py $input_TP_4 $output_path_TP_4 &

# Centromeres and Telomeres:
python Centro_Telo_match2.py $input_TP_4 $output_path_TP_4 &

# GCcontent:
python GCcontent2.py $input_TP_4 $output_path_TP_4 &

# Sequence Complexity:
python SeqComplexity.py $input_TP_4 $output_path_TP_4 &

# Replication Time #NOT USED
#python Replication_Time2.py $input_TP_4 $output_path_TP_4 

# Recombination Rate: #(WARRING - RISK OF MISSING DATA!)
python Recombination_Rate2.py $input_TP_4 $output_path_TP_4 &

#Introns and Exons coverage:
python Genes_V3.py $input_TP_4 $output_path_TP_4 &

# Lamina Associated domains:
python Lamina_Associ_Dom.py $input_TP_4 $output_path_TP_4 &

# CpG island distance:
python CpG_island2.py $input_TP_4 $output_path_TP_4 &

# TAD Boundaries:
python TADs2.py $input_TP_4 $output_path_TP_4 &


wait
echo "Dels data ready!!!"  
echo "Assembling dataset!"
python makedataset-deletions.py $output_path_TP_4 $output_path_TP_4 
echo "Start predicting!"
python predictClassify.py $output_path_TP_4 DEL $output_path_TP_4
echo "Done!"