2. Usage

Usage

python CTADO.py <clr1> <clr2> <resolution> <window> <flank> <binsize> <clr1_boundaries> <clr2_boundaries> [options]

Run command below to see usage and arguments:

python CTADO.py -h

Positional arguments

• clr1_filename : name of first contact matrix in mcool/cool format
• clr2_filename : name of first contact matrix in mcool/cool format
• resolution : resolution of mcool file
• window : size of the sliding diamond window
• flank : flank size in bp
• binsize : bin size in bp
• clr1_boundaries_name : the first contact matrix boundaries argument, a dataframe name with TADs boundaries in chrom, start, end format or cooler insulation table
• clr2_boundaries_name : the second contact matrix boundaries argument, a dataframe name with TADs boundaries in chrom, start, end format or cooler insulation table

Note:

It is possible to create cooler insulation table based on contact matrix in mcool/cool format if you do not have one.

Use command below:

python -c 'from src.calculate_intensity_change import get_boundaries; get_boundaries(<clr>, <resolution>, <window>)'

Options

• -h, --help : show this help message and exit
• -r1, --result_df_1_name : The first contact matrix dataframe name with chrom, start & end of TADs boundary
• -r2, --result_df_2_name : The second contact matrix dataframe name with chrome, start & end of TADs boundary
• -df, --result_dataframe_name : Dataframe name with intersecting TADs of two contact matrixes
• -od, --output_directory: The path to the save directory
• -nc, --number_of_charts: The number of output charts for each type of change. If the specified number is greater than the number of events, then all of them will be output. If number is -1 than all of them will be output. (default: 5)
• -lg, --logging {True,False}: Enables logging (default: False)
• -t, --threads: Parameter for specifying the number of threads (default: 1)