#!/usr/bin/env bash

# minimum target set size (as a percentage of total # input sequence regions)
min_target_set_size_percentage_threshold=0.001

# se tot 'yes' if permutationa filter is to be applied and 'no' otherwise
use_permutation_filter=yes
# number standard deviations relative to the mean of the null scores distribution
siginficance_threshold=3.0

##########################################
# regression estimation parameters
##########################################
# 'yes' -> regression scoring of target set
# 'no'  -> scoring of target set as described in the cERMIT paper
use_regression_scoring=yes

# input covariates file
covariates_file=covariates/MM1
##########################################
in_seeds_file=miRbase_sorted

# output directory
# NB: relative path to the $data_directory 
#out_dir=out_"$annot"_regression_"$use_regression_scoring"_seeds_miRbase_sorted
#out_dir=out_regression_"$use_regression_scoring"_seeds_"$in_seeds_file"
out_dir=out_seeds_"$in_seeds_file"

executable=./mEAT
# values corresponding to high evidence of binding, e.g. transform: p-value -> -log[p-value]
evidence_file_list=evidence_file_list
# file containing information on the input sequence
sequence_file_list=sequence_file_list

##########################################
# DO NOT MODIFY BEYOND THIS POINT !!!!!!!!
##########################################
echo "output directory: $out_dir"
$executable $evidence_file_list $sequence_file_list $out_dir $in_seeds_file $min_target_set_size_percentage_threshold $use_regression_scoring $covariates_file $siginficance_threshold $use_permutation_filter