metaloci.utility_scripts package

Subset of modules to run some utility scripts, useful for METALoci but that are not part of the main pipeline.

Submodules

metaloci.utility_scripts.bts module

Find the best combination persistence length and cut-off for your Hi-C, given a Hi-C resolution.

Check first the maximum resolution yout Hi-C allows, and supply it to this script. This script will then determine, by computing layouts on a sample of regions, the best combination of persistence length and cut-off for your Hi-C. You can then use these parameters to run ‘metaloci layout’ on your regions of interest.

This can take from minutes to a few hours, depending on the resolution, the size of the regions and the number of cpu’s available in your machine. Once you run it for a specific Hi-C and a specific resolution, the parameters will remain the same for other runs with other signals.

metaloci.utility_scripts.bts.bts_ratio(hic_path: str, resolution: int, region: str, cutoff: float, pl: float) → float

Calculate the ratio of the correlation between the linear and spherical layouts against the layout we actually want to use. This is a good mesure to estimate the best set of parameters for the Kamada-Kawai layout.

Returns:

linear_correlation / spherical_correlation – Ratio of the correlation between the linear and spherical layouts.

Return type:

float

Test METALoci parameters to optimise Kamada-Kawai layout.

Parameters:

  • row (pd.Series) – Row of the region file.

  • args (pd.Series) – Arguments to test.

  • progress (mp.Manager().dict) – Progress bar.

metaloci.utility_scripts.bts.pl_estimation(row: Series, args: Series, progress=None) → float

Wrapper function to count the number of interacctions in a subseted Hi-C matrix.

Parameters:

  • row (pd.Series) – Row of the region file.

  • args (pd.Series) – Arguments to test.

  • progress (mp.Manager().dict) – Progress bar.

Returns:

sum_dict – Dictionary with the sum of interactions for each set of parameters

Return type:

dict

metaloci.utility_scripts.bts.run(opts: list)

Main function to run bts.

Parameters:

opts (list) – List of arguments

metaloci.utility_scripts.bts.sum_hic_columns(hic_path: str, resolution: int, region: str, cutoff: float) → float

Function to count the number of interacctions in a subseted Hi-C matrix.

Parameters:

  • hic_path (str) – Path to the Hi-C file.

  • resolution (int) – Resolution of the Hi-C file.

  • region (tuple) – Region of interest.

  • cutoff (float) – Cutoff to use for the subset matrix.

Returns:

median_sum – Median sum of the interactions in the subset matrix.

Return type:

float

metaloci.utility_scripts.gene_selector module

This script parses the LMI information files created by METALoci.

The output file will contain regions that pass the quadrant and p-value threshold for a given signal. In case it doesn’t pass this filters, the script will output NA.

metaloci.utility_scripts.gene_selector.run(opts: list)

Funtion to run this section of METALoci with the needed arguments

Parameters:

opts (list) – List of arguments

metaloci.utility_scripts.sniffer module

Takes a .gft file or a .bed file and parses it into a region list, with a specific resolution and extension. The point of interest of the regions is the middle bin.

metaloci.utility_scripts.sniffer.run(opts: list)

Funtion to run this section of METALoci with the needed arguments.

Parameters:

opts (list) – List of arguments.