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Prepare Decoding API

Import everything from the module:

Main prepare_decoding method

The module asmc.preparedecoding contains a method prepare_decoding with the following signature:

def prepare_decoding(
        demography: str,
        discretization: Union[list, str],
        frequencies: str,
        csfs_file: str = "",
        samples: int = 300,
        mutation_rate: float = 1.65e-8,
) -> DecodingQuantities

Demography

The demography is either a path to a demography file (see file formats) or a three-letter code representing a built-in demography.

Supported built-in demographies can be one of:

ACB, ASW, BEB, CDX, CEU, CHB, CHS, CLM, ESN, FIN, GBR, GIH, GWD, IBS, ITU, JPT, KHV, LWK, MSL, MXL, PEL, PJL, PUR, STU, TSI, YRI.

Discretization

The discretization is either a path to a discretization file (see file formats) or a discretization specification.

A discretization specification allows you to build a discretization with fixed values for recent times with optional additional values calculated at runtime from the coalescent distribution. This is specified as a list of lists, with an optional final integer, e.g.:

  • [[30.0, 10]] will create a discretization with 10 intervals of size 30
  • [[30.0, 10], [100.0, 8]] will create a discretization with 10 intervals of size 30, followed by 8 intervals of size 100
  • [[30.0, 10], [100.0, 8], 25] will create a discretization with 10 intervals of size 30, followed by 8 intervals of size 100, followed by 25 additional intervals calculated from the coalescent distribution

Frequencies

The frequencies parameter is either a path to a frequencies file (see file formats) or a built-in code.

Currently, the only built-in available is 'UKBB', which uses built-in frequency information from the UK BioBank, if and only if the number of samples is one of {50, 100, 200, 300}.

Csfs file

An optional path to a CSFS file. If omitted, the CSFS will be calculated at runtime.

Samples

The number of samples, with a default value of 300.

Mutation rate

The mutation rate, with a default value of 1.65e-8.

The DecodingQuantities object

Calling prepare_decoding returns a DecodingQuantities object. This can be explored, if you wish; see the example notebook.

Methods on this object allow you to save information to various files. For a DecodingQuantities object dq you can:

  • Create a file dir/output.decodingQuantities.gz:

    dq.save_decoding_quantities('dir/output')

  • Create a file dir/output.csfs:

    dq.save_csfs('dir/output')

  • Create a file dir/output.intervalsInfo:

    dq.save_intervals('dir/output')

  • Create a file dir/output.disc:

    dq.save_discretization('dir/output')

Other methods

You can save an in-built demography to file:

  • Create file dir/CEU.demo: 
    save_demography('dir/', 'CEU')