polychrom.legacy.contactmaps module

This file contains a bunch of method to work on contact maps of a Hi-C data.

polychrom.legacy.contactmaps.averageBinnedContactMap(filenames, chains=None, binSize=None, cutoff=1.7, n=4, loadFunction=<function load>, exceptionsToIgnore=None, printProbability=1, map_function=<class 'map'>)

Returns an average contact map of a set of conformations. Non-existing files are ignored if exceptionsToIgnore is set to IOError. example:

An example:

Parameters:

• filenames (list of strings) – Filenames to average map over
• chains (list of tuples or Nx2 array) – (start,end+1) of each chain
• binSize (int) – size of each bin in monomers
• cutoff (float, optional) – Cutoff to calculate contacts
• n (int, optional) – Number of threads to use. By default 4 to minimize RAM consumption.
• exceptionsToIgnore (list of Exceptions) – List of exceptions to ignore when finding the contact map. Put IOError there if you want it to ignore missing files.

Returns:

• tuple of two values
• (i) MxM numpy array with the conntact map binned to binSize resolution.
• (ii) chromosomeStarts a list of start sites for binned map.

polychrom.legacy.contactmaps.averagePureContactMap(filenames, cutoff=1.7, n=4, loadFunction=<function load>, exceptionsToIgnore=[], printProbability=0.005, map_function=<class 'map'>)

Parameters

filenames : list of strings

Filenames to average map over

cutoff : float, optional

Cutoff to calculate contacts

n : int, optional

Number of threads to use. By default 4 to minimize RAM consumption with pure maps.

exceptionsToIgnore : list of Exceptions

List of exceptions to ignore when finding the contact map. Put IOError there if you want it to ignore missing files.

Returns:An NxN (for pure map) numpy array with the contact map.

polychrom.legacy.contactmaps.pureMap(data, cutoff=1.7, contactMap=None)

calculates an all-by-all contact map of a single polymer chain. Doesn’t work for multi-chain polymers!!! If contact map is supplied, it just updates it

Parameters:

• data (Nx3 or 3xN array) – polymer conformation
• cutoff (float) – cutoff for contacts
• contactMap (NxN array, optional) – contact map to update, if averaging is used

polychrom.legacy.contactmaps.rescalePoints(points, bins)

converts array of contacts to the reduced resolution contact map

polychrom.legacy.contactmaps.rescaledMap(data, bins, cutoff=1.7, contactMap=None)

calculates a rescaled contact map of a structure :param data: polymer conformation :type data: Nx3 or 3xN array :param bins: bin starts :type bins: Lx1 array :param cutoff: cutoff for contacts :type cutoff: float, optional

Returns:resXres array with the contact map