DNA-seq reads/counts

sistem.data.gen_readcounts_singlecell(tree: Tree, params: Parameters | None = None, out_dir: str | None = None, coverage: float | None = None, bin_size: int | None = None, read_len: int | None = None, lorenz_y: float | None = None, lorenz_x: float = 0.5)

Given a Tree object returned by GrowthSimulator.simulate_singlecell_lineage, compiles cell-specific region-level copy numbers and draws allele-specific read counts. These will automatically be saved in the output directory. See Parameters for an explanation of the parameters.

Parameters:

  • tree (Tree)

  • params (Parameters, optional)

  • out_dir (str, optional)

  • coverage (float, optional)

  • bin_size (int, optional)

  • read_len (int, optional)

  • lorenz_y (float, optional)

Returns:

A dictionary where keys are cells and values are a dictionary containing the region-level allele-specific copy numbers.

Return type:

dict

sistem.data.gen_readcounts_bulk(tree: Tree, params: Parameters | None = None, out_dir: str | None = None, coverage: float | None = None)

Given a Tree object returned by GrowthSimulator.simulate_clonal_lineage, draws a total and variant read count for each site at every SNV position in the observed cells. These will automatically be saved in the output directory. See Parameters for an explanation of the parameters.

Parameters:

  • tree (Tree)

  • params (Parameters, optional)

  • out_dir (str, optional)

  • coverage (float, optional)

sistem.data.gen_reads(tree: Tree, params: Parameters | None = None, out_dir: str | None = None, ref: str | None = None, alt_ref: str | None = None, coverage: float | None = None, bin_size: int | None = None, read_len: int | None = None, lorenz_y: float | None = None, num_processors: int | None = None, lorenz_x: float = 0.5)

Given a Tree object returned by GrowthSimulator.simulate_singlecell_lineage, generates synthetic paired-end DNA sequencing reads for each cell. Requires the dwgsim and samtools binaries be available in the user’s $PATH variable. Will create two fastq files for each cell located in the ‘reads’ directory within the provided output directory. See Parameters for an explanation of the parameters.

Parameters:

  • tree (Tree)

  • params (Parameters, optional)

  • out_dir (str, optional)

  • ref (str, optional)

  • alt_ref (str, optional)

  • coverage (float, optional)

  • bin_size (int, optional)

  • read_len (int, optional)

  • lorenz_y (float, optional)

  • num_processors (int, optional)