parameters.txt

# Data input path
# For dense type, input_path should be the root directory of the dense chromatin contact matrix. The dense matrices are named as chr*_dense_matrix.bed, where * represents the chromosome number. Each dense matrix is a non-negative symmetric matrix of size N x N, where N represents bin number.
# For sparse type, input_path should be the root directory of the sparse chromatin contact matrix. The sparse matrices are named as chr*_sparse_matrix.bed, where * represents the chromosome number. Each sparse matrix is a matrix of size N x 3, where N represents bin number, The first two columns represent the indices of the bins, while the third column represents the interaction count between these two bins. 
# For cool、mcool、hic, input_path should be the file name with detailed path.
input_path = /mnt/disk2/ddc/project/TADGATE/Data_for_packages/GSM7682228_K562_cell_062.hic

# Data type [dense sparse mcool hic]
dtype = hic

# Chromosome number(s): Input the chromosome number(s) needed for calculation. It can be individual numbers or a range.
#chr_num = 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X
chr_num = 1,2,

# Data resolution (bin/bp)
resolution = 50000

# chromosome size file for your reference genome, the first column is the chromosome identifier, and the second column is the chromosome length, such as chr1 249250621.
chr_size_file = /mnt/disk2/ddc/project/TADGATE/Data_for_packages/chrom_hg38_sizes.txt


# parameters for graph attention auto-encoder. 
device = cuda:0
graph_radius = 2
split_size = all
layer_node1 = 500
layer_node2 = 100
embed_attention = False
lr = 0.001
weight_decay = 0.0001
num_epoch = 500
weight_use = Fix
weight_rate = 0.5
weight_range = 100
impute_func = True
impute_range = 5


# paramaters for TAD detection
bd_weight_list = [1.5, 1.5, 1, 1]
cluster_method = K-means
wd_ci = 5
wd_p = 3
dist = 3
window_range = 5000000
pvalue_cut = 0.05
exp_length = 500000
length_cut = 3
filter_method = strict


# result save path
output_path = /mnt/disk2/ddc/project/TADGATE/Data_for_packages/Result_test
save_att_mat = False