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scATAC-seq/scripts/10xgenomics_PBMC_5k_peaks_classification_1/classification_peaks.sh
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classification_peaks.sh
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# some paths
## directories
results_dir='results/10xgenomics_PBMC_5k_peaks_classification_1'
data_dir='results/10xgenomics_PBMC_5k'
## input
file_mat_open="$data_dir/peaks_open_bin1bp_read_atac.mat"
file_mat_nucl="$data_dir/peaks_nucleosomes_bin1bp_read_atac.mat"
file_mat_seq="$data_dir/peaks_sequences.mat"
## file with seeds
file_seed=$results_dir'/peaks_seed.txt'
mkdir -p $results_dir
touch $file_seed
# parameters
n_iter='20'
n_shift='201'
seeding='random'
n_core=8
# open chromatin and nucleosomes
# for k in 10 20 30
# do
# seed=$(< /dev/urandom tr -dc _A-Z-a-z-0-9 | head -c${1:-15};echo)
# file_prob=$results_dir/'peaks_sequences_'$k'class_prob.mat4d'
# file_mod1=$results_dir/'peaks_openchromatin_bin1bp_'$k'class_model.mat'
# file_mod2=$results_dir/'peaks_nucleosomes_bin1bp_'$k'class_model.mat'
# file_mod3=$results_dir/'peaks_sequences_'$k'class_model.mat'
# echo "$file_prob $seed" >> $file_seed
# bin/ChIPPartitioning --seq $file_mat_seq --class $k --shift $n_shift --flip --iter $n_iter --seeding $seeding --seed $seed --thread $n_core > $file_prob
# bin/ProbToModel --read $file_mat_open --prob $file_prob --thread $n_core 1> $file_mod1
# bin/ProbToModel --read $file_mat_1nucl --prob $file_prob --thread $n_core 1> $file_mod2
# bin/ProbToModel --read $file_mat_nucl --prob $file_prob --thread $n_core 1> $file_mod3
# bin/ProbToModel --seq $file_mat_seq --prob $file_prob --thread $n_core 1> $file_mod4
# done
k=5
seed=$(< /dev/urandom tr -dc _A-Z-a-z-0-9 | head -c${1:-15};echo)
file_prob=$results_dir/'peaks_sequences_'$k'class_prob.mat4d'
file_mod1=$results_dir/'peaks_openchromatin_bin1bp_'$k'class_model.mat'
file_mod2=$results_dir/'peaks_nucleosomes_bin1bp_'$k'class_model.mat'
file_mod3=$results_dir/'peaks_sequences_'$k'class_model.mat'
echo "$file_prob $seed" >> $file_seed
bin/ChIPPartitioning --seq $file_mat_seq --class $k --shift $n_shift --flip --iter $n_iter --seeding $seeding --seed $seed --thread $n_core > $file_prob
bin/ProbToModel --read $file_mat_open --prob $file_prob --thread $n_core 1> $file_mod1
bin/ProbToModel --read $file_mat_1nucl --prob $file_prob --thread $n_core 1> $file_mod2
bin/ProbToModel --read $file_mat_nucl --prob $file_prob --thread $n_core 1> $file_mod3
bin/ProbToModel --seq $file_mat_seq --prob $file_prob --thread $n_core 1> $file_mod4
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