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

cutofffloat, optional

Cutoff to calculate contacts

nint, optional

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

exceptionsToIgnorelist 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