Source code for shephard.tools.site_tools

"""
SHEPHARD: 
Sequence-based Hierarchical and Extendable Platform for High-throughput Analysis of Region of Disorder

Authors: Garrett M. Ginell & Alex S. Holehouse
Contact: (g.ginell@wustl.edu)

Holehouse Lab - Washington University in St. Louis
"""

from shephard import general_utilities
import numpy as np

[docs]def build_site_density_vector(protein, site_types=None, window_size=30, append_leading_lagging=True): """ Function that constructs a sliding-window density vector of sites along a protein. site_types is a list of one or site types. This tool is stateless - i.e. it does not alter the passed protein but instead only generates a numerical list which could be added as a track. Parameters ---------------- protein : shephard.protein.Protein object Protein object over which sites are identified site_type : str or list of strings One or more possible site_types that may be found in the protein. Either a single string or a list of strings can be passed, allowing for one or more sites to be grouped together window_size : int Size of sliding window over which site density is calculated append_leading_lagging : Bool Flag that if true will mean the function returns a numerical vector equal in length of the protein. If false, will return a shorter vector and not add leading/lagging values. Returns ------------- list Returns a list of values equal to the length of the protein, where the value at each position reports on the local denisty of sites averaged over the window_size. """ # give ability to take a single string or a list of strings if we wish # to compare against multype site types if site_types is not None: site_types = general_utilities.string_to_list_of_strings(site_types) nres = len(protein) # first build an empty vector of 0s equal to the length of the sequence all_res = [0]*len(protein) # then for each site assign a '1' to positions where a site exists for position in protein.site_positions: sites = protein.site(position) # if we didn't specifit a site type assume all sites are fair game if site_types is None: all_res[position - 1] = 1 # else validate against the set of available sites and IF the site # matches the requested else: # for every site object found at $position for s in sites: if s.site_type in site_types: all_res[position - 1] = 1 # finally we're going to calculate the density of sites from this vector # note we're treating site presence as a binary phenomenon - ie a residue # has a site or does not density_vector = [] for pos in range(0, (nres - window_size)+1): local_density = np.sum(all_res[pos:pos+window_size])/window_size density_vector.append(local_density) # having built a density vector that is nres-window_size+1 in length, we now need to extend the N and C # termini such that the len(denisty_vector) = len(protein) # this code creates leading/lagging values to fill in the missing ones such that the actual value # of the density vector reports on the density half-way across the window_size and the # track length = nres leading_values = [density_vector[0]]*int(window_size/2) lagging_values = [density_vector[-1]]*(nres - (len(density_vector) + len(leading_values))) # this line then combines the leading, desnity and lagging lists into a single list, and we # then add this numerical list as a track final = leading_values + density_vector + lagging_values return final