reconstruction.ecoli.dataclasses.process.replication
SimulationData for replication process
- class reconstruction.ecoli.dataclasses.process.replication.Replication(raw_data, sim_data)[source]
Bases:
object
SimulationData for the replication process
- _build_motifs(raw_data, sim_data)[source]
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)[source]
Build replication-associated simulation data from raw data.
- _build_sites(raw_data, sim_data)[source]
Build simulation data associated with DNA sites from raw_data.
- _get_complement_sequence(sequenceVector)[source]
Calculates the vector for a complement sequence of a DNA sequence given in vector form.
- _get_motif_coordinates(motif_length, motif_sequences)[source]
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)[source]
Converts an array of genomic coordinates into coordinates relative to the origin of replication.