# some paths
## directories
results_dir='results/10xgenomics_PBMC_5k_classification_1'
data_dir='results/10xgenomics_PBMC_5k'
## input
file_mat_open="$data_dir/ebf1_motifs_10e-6_open_bin1bp_read_atac.mat"
file_mat_1nucl="$data_dir/ebf1_motifs_10e-6_1nucl_bin1bp_fragment_center.mat"
## file with seeds
file_seed=$results_dir'/ebf1_motifs_10e-6_seed.txt'

mkdir -p $results_dir
touch $file_seed

# parameters
n_iter='20'
n_shift='21'
seeding='random'
n_core=3

# open chromatin
for k in 1 2 3 4 5 6 7 8 9 10
do
	seed=$(< /dev/urandom tr -dc _A-Z-a-z-0-9 | head -c${1:-15};echo)
	file_prob=$results_dir/'ebf1_motifs_10e-6_open_bin1bp_read_atac_'$k'class_prob.mat4d'
	file_ref1=$results_dir/'ebf1_motifs_10e-6_open_bin1bp_read_atac_'$k'class_ref.mat'
	file_ref2=$results_dir/'ebf1_motifs_10e-6_open_bin1bp_read_atac_'$k'class_1nucl_fragment_center_ref.mat'
	file_aic=$results_dir/'ebf1_motifs_10e-6_open_bin1bp_read_atac_'$k'class_aic.txt'
	echo "$file_prob $seed" >> $file_seed
	bin/ChIPPartitioningNew --read $file_mat_open  --class $k --shift $n_shift --flip --iter $n_iter --seeding $seeding --seed $seed > $file_prob
	bin/probToRefNew        --read $file_mat_open  --prob $file_prob --parallel $n_core 1> $file_ref1
	bin/probToRefNew        --read $file_mat_1nucl --prob $file_prob --parallel $n_core 1> $file_ref2
done

# 1nucl chromatin
for k in 1 2 3 4 5 6 7 8 9 10
do
	seed=$(< /dev/urandom tr -dc _A-Z-a-z-0-9 | head -c${1:-15};echo)
	file_prob=$results_dir/'ebf1_motifs_10e-6_1nucl_bin1bp_fragment_center_'$k'class_prob.mat4d'
	file_ref1=$results_dir/'ebf1_motifs_10e-6_1nucl_bin1bp_fragment_center_'$k'class_ref.mat'
	file_ref2=$results_dir/'ebf1_motifs_10e-6_1nucl_bin1bp_fragment_center_'$k'class_open_read_atac_ref.mat'
	file_aic=$results_dir/'ebf1_motifs_10e-6_1nucl_bin1bp_fragment_center_'$k'class_aic.txt'
	echo "$file_prob $seed" >> $file_seed
	bin/ChIPPartitioningNew --read $file_mat_1nucl --class $k --shift $n_shift --flip --iter $n_iter --seeding $seeding --seed $seed > $file_prob
	bin/probToRefNew        --read $file_mat_1nucl --prob $file_prob --parallel $n_core 1> $file_ref1
	bin/probToRefNew        --read $file_mat_open  --prob $file_prob --parallel $n_core 1> $file_ref2
done