reconstruction.ecoli.dataclasses.process.replication

SimulationData for replication process

class reconstruction.ecoli.dataclasses.process.replication.Replication(raw_data, sim_data)

Bases: object

SimulationData for the replication process

_build_elongation_rates(raw_data, sim_data)

_build_gene_data(raw_data, sim_data)

Build gene-associated simulation data from raw data.

_build_motifs(raw_data, sim_data)

Build simulation data associated with sequence motifs from raw_data. Coordinates of all motifs are calculated based on the given sequences of the genome and the motifs.

_build_replication(raw_data, sim_data)

Build replication-associated simulation data from raw data.

_build_sequence(raw_data, sim_data)

_build_sites(raw_data, sim_data)

Build simulation data associated with DNA sites from raw_data.

_get_complement_sequence(sequenceVector)

Calculates the vector for a complement sequence of a DNA sequence given in vector form.

_get_motif_coordinates(motif_length, motif_sequences)

Finds the coordinates of all sequence motifs of a specific type. The coordinates are given as the positions of the midpoint of the motif relative to the oriC in base pairs.

_get_relative_coordinates(coordinates)

Converts an array of genomic coordinates into coordinates relative to the origin of replication.

get_average_copy_number(tau, coords)

Calculates the average copy number of a gene throughout the cell cycle given the location of the gene in coordinates.

Parameters:

• tau (float) – expected doubling time in minutes

• coords (int or ndarray[int]) – chromosome coordinates of genes

Returns:

average copy number of each gene expected at a doubling time, tau

Return type:

float or ndarray[float] (matches length of coords)

make_elongation_rates(random, replisomes, base, time_step)

exception reconstruction.ecoli.dataclasses.process.replication.SiteNotFoundError

Bases: Exception