# paths
## dir
data_dir="data/10xgenomics_PBMC_5k_peaks"
pwm_dir="data/pwm/jaspar_2018_clustering/"
results_dir="results/10xgenomics_PBMC_5k_peaks_classification_4"
## matrix files
file_mat_open=$data_dir/'peaks_rmsk_sampled_openchromatin_1kb_read_atac.mat'
file_mat_nucl=$data_dir/'peaks_rmsk_sampled_nucleosomes_1kb_fragment_center.mat'
file_mat_seq=$data_dir/'peaks_rmsk_sampled_sequences_1kb.mat'
## file with seeds
file_seed=$results_dir'/peaks_rmsk_sampled_seed.txt'

mkdir -p $results_dir
touch $file_seed

# EM param
n_iter='100'
n_shift='971'
n_core=32
## PWM files
jun="$pwm_dir/cluster_3_node_23_20_motifs_prob.mat"
hif1a="$pwm_dir/cluster_4_node_31_3_motifs_prob.mat"
myc="$pwm_dir/cluster_4_node_22_4_motifs_prob.mat"
pu1="$pwm_dir/cluster_7_node_13_2_motifs_prob.mat"
cebpb="$pwm_dir/cluster_5_node_20_5_motifs_prob.mat"
irf4="$pwm_dir/cluster_31_node_4_5_motifs_prob.mat"
irf2="$pwm_dir/cluster_31_node_5_2_motifs_prob.mat"
lhx3="$pwm_dir/cluster_1_node_74_2_motifs_prob.mat"
foxh1="$pwm_dir/cluster_66_1_motifs_prob.mat"
sox3="$pwm_dir/cluster_33_node_1_2_motifs_prob.mat"
mef2c="$pwm_dir/cluster_20_4_motifs_prob.mat"
elf5="$pwm_dir/cluster_7_node_17_5_motifs_prob.mat"
stat6="$pwm_dir/cluster_32_node_STAT6_1_motifs_prob.mat"
nfe2="$pwm_dir/cluster_3_node_24_4_motifs_prob.mat"
ahr="$pwm_dir/cluster_4_node_30_2_motifs_prob.mat"
e2f2="$pwm_dir/cluster_39_node_1_2_motifs_prob.mat"
ctcf="$pwm_dir/cluster_48_node_ctcf_1_motifs_prob.mat"


# classify
for k in 17 20 30
do
	## results files
	file_prob=$results_dir/'peaks_rmsk_sampled_sequences_1kb_'$k'class_prob.mat4d'
	file_mod1=$results_dir/'peaks_rmsk_sampled_openchromatin_1kb_read_atac_'$k'class_model.mat'
	file_mod2=$results_dir/'peaks_rmsk_sampled_nucleosomes_1kb_fragment_center_'$k'class_model.mat'
	file_mod3=$results_dir/'peaks_rmsk_sampled_sequences_1kb_'$k'class_model.mat'	
	seed=$(< /dev/urandom tr -dc _A-Z-a-z-0-9 | head -c${1:-15};echo)
	echo "$file_prob $seed" >> $file_seed
	bin/EMSequence  --seq  $file_mat_seq --class $k --motifs $jun,$hif1a,$myc,$pu1,$cebpb,$irf4,$irf2,$lhx3,$foxh1,$sox3,$mef2c,$elf5,$stat6,$nfe2,$ahr,$e2f2,$ctcf --shift $n_shift --flip --iter $n_iter --seed $seed --thread $n_core --out $file_prob
	bin/ProbToModel --read $file_mat_open --prob $file_prob --thread $n_core 1> $file_mod1
	bin/ProbToModel --read $file_mat_nucl --prob $file_prob --thread $n_core 1> $file_mod2
	bin/ProbToModel --seq  $file_mat_seq  --prob $file_prob --thread $n_core 1> $file_mod3
done