Command-line options

Command line interface for stdpopsim.

usage: stdpopsim [-h] [-V] [-v | -q] [-c CACHE_DIR] [-e {msprime,slim}]
                 [--msprime-model {hudson,dtwf,smc,smc_prime}]
                 [--msprime-change-model T MODEL] [--slim-path PATH]
                 [--slim-script] [--slim-scaling-factor Q] [--slim-burn-in X]
                 {AraTha,CanFam,DroMel,EscCol,HomSap,PonAbe,download-genetic-maps}
                 ...

Positional Arguments

subcommand

Possible choices: AraTha, CanFam, DroMel, EscCol, HomSap, PonAbe, download-genetic-maps

Named Arguments

-V, --version

show program’s version number and exit

-v, --verbose

Increase logging verbosity (can use be used multiple times).

Default: 1

-q, --quiet

Do not write any non-essential messages

-c, --cache-dir

Set the cache directory to the specified value. Note that this can also be set using the environment variable STDPOPSIM_CACHE. If both the environment variable and this option are set, the option takes precedence. Default: /home/docs/.cache/stdpopsim

-e, --engine

Possible choices: msprime, slim

Specify a simulation engine.

Default: “msprime”

msprime specific parameters

--msprime-model

Possible choices: hudson, dtwf, smc, smc_prime

Specify the simulation model used by msprime. See msprime API documentation for details.

Default: “hudson”

--msprime-change-model

Change to the specified simulation MODEL at generation T. This option may provided multiple times.

Default: []

SLiM specific parameters

--slim-path

Full path to `slim’ executable.

--slim-script

Write script to stdout and exit without running SLiM.

Default: False

--slim-scaling-factor

Rescale model parameters by Q to speed up simulation. See SLiM manual: 5.5 Rescaling population sizes to improve simulation performance. [default=1].

Default: 1

--slim-burn-in

Length of the burn-in phase, in units of N generations [default=10].

Default: 10

Sub-commands:

AraTha

Run simulations for Arabidopsis thaliana using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Arabidopsis thaliana: Generation time: 1.0 Population size: 10000 Mutation rate: 7e-09 Recombination rate: 8.029378384412594e-10

stdpopsim AraTha [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
                 [--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g] [-c]
                 [-l LENGTH_MULTIPLIER] [-s SEED] [-d] [-o OUTPUT]
                 samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

--help-genetic-maps

Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps

-D, --dry-run

Do not run actual simulation

Default: False

-g, --genetic-map

Possible choices: SalomeAveraged_TAIR7

Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://stdpopsim.readthedocs.io/en/latest/catalog.html> Available maps: SalomeAveraged_TAIR7.

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, Mt, Pt

Simulate a specific chromosome. Options: 1, 2, 3, 4, 5, Mt, Pt. Default=1.

Default: “1”

-l, --length-multiplier

Simulate a sequence of length l times the named chromosome’s length, using the named chromosome’s mutation and recombination rates.

Default: 1

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

-d, --demographic-model

Possible choices: SouthMiddleAtlas_1D17, African2Epoch_1H18, African3Epoch_1H18

Specify a simulation model. If no model is specified, a single populationconstant size model is used. Available models:SouthMiddleAtlas_1D17, African2Epoch_1H18, African3Epoch_1H18. Please see –help-models for details of these models.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

CanFam

Run simulations for Canis familiaris using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Canis familiaris: Generation time: 3 Population size: 13000 Mutation rate: 4e-09 Recombination rate: 9.506415406601852e-09

stdpopsim CanFam [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
                 [--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g] [-c]
                 [-l LENGTH_MULTIPLIER] [-s SEED] [-d] [-o OUTPUT]
                 samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

--help-genetic-maps

Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps

-D, --dry-run

Do not run actual simulation

Default: False

-g, --genetic-map

Possible choices: Campbell2016_CanFam3_1

Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://stdpopsim.readthedocs.io/en/latest/catalog.html> Available maps: Campbell2016_CanFam3_1.

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, X, MT

Simulate a specific chromosome. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, X, MT. Default=1.

Default: “1”

-l, --length-multiplier

Simulate a sequence of length l times the named chromosome’s length, using the named chromosome’s mutation and recombination rates.

Default: 1

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

-d, --demographic-model

Specify a simulation model. If no model is specified, a single populationconstant size model is used. Available models:. Please see –help-models for details of these models.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

DroMel

Run simulations for Drosophila melanogaster using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Drosophila melanogaster: Generation time: 0.1 Population size: 1720600 Mutation rate: 5.49e-09 Recombination rate: 8.174875882734035e-09

stdpopsim DroMel [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
                 [--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g] [-c]
                 [-l LENGTH_MULTIPLIER] [-s SEED] [-d] [-o OUTPUT]
                 samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

--help-genetic-maps

Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps

-D, --dry-run

Do not run actual simulation

Default: False

-g, --genetic-map

Possible choices: ComeronCrossover_dm6

Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://stdpopsim.readthedocs.io/en/latest/catalog.html> Available maps: ComeronCrossover_dm6.

-c, --chromosome

Possible choices: 2L, 2R, 3L, 3R, 4, X, Y, mitochondrion_genome

Simulate a specific chromosome. Options: 2L, 2R, 3L, 3R, 4, X, Y, mitochondrion_genome. Default=2L.

Default: “2L”

-l, --length-multiplier

Simulate a sequence of length l times the named chromosome’s length, using the named chromosome’s mutation and recombination rates.

Default: 1

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

-d, --demographic-model

Possible choices: African3Epoch_1S16, OutOfAfrica_2L06

Specify a simulation model. If no model is specified, a single populationconstant size model is used. Available models:African3Epoch_1S16, OutOfAfrica_2L06. Please see –help-models for details of these models.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

EscCol

Run simulations for Escherichia coli using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Escherichia coli: Generation time: 3.805175e-05 Population size: 180000000.0 Mutation rate: 0.00021 Recombination rate: 0.0

stdpopsim EscCol [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                 [-l LENGTH_MULTIPLIER] [-s SEED] [-d] [-o OUTPUT]
                 samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-l, --length-multiplier

Simulate a sequence of length l times the named chromosome’s length, using the named chromosome’s mutation and recombination rates.

Default: 1

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

-d, --demographic-model

Specify a simulation model. If no model is specified, a single populationconstant size model is used. Available models:. Please see –help-models for details of these models.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

HomSap

Run simulations for Homo sapiens using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘–output’ option to specify a filename.

Default population parameters for Homo sapiens: Generation time: 30 Population size: 10000 Mutation rate: 1.2899999999999998e-08 Recombination rate: 1.2051790226570845e-08

stdpopsim HomSap [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
                 [--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g] [-c]
                 [-l LENGTH_MULTIPLIER] [-s SEED] [-d] [-o OUTPUT]
                 samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

--help-genetic-maps

Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps

-D, --dry-run

Do not run actual simulation

Default: False

-g, --genetic-map

Possible choices: HapMapII_GRCh37, DeCodeSexAveraged_GRCh36, PyrhoACB_GRCh37, PyrhoASW_GRCh37, PyrhoBEB_GRCh37, PyrhoCDX_GRCh37, PyrhoCEU_GRCh37, PyrhoCHB_GRCh37, PyrhoCHS_GRCh37, PyrhoCLM_GRCh37, PyrhoESN_GRCh37, PyrhoFIN_GRCh37, PyrhoGBR_GRCh37, PyrhoGIH_GRCh37, PyrhoGWD_GRCh37, PyrhoIBS_GRCh37, PyrhoITU_GRCh37, PyrhoJPT_GRCh37, PyrhoKHV_GRCh37, PyrhoLWK_GRCh37, PyrhoMSL_GRCh37, PyrhoMXL_GRCh37, PyrhoPEL_GRCh37, PyrhoPJL_GRCh37, PyrhoPUR_GRCh37, PyrhoSTU_GRCh37, PyrhoTSI_GRCh37, PyrhoYRI_GRCh37

Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://stdpopsim.readthedocs.io/en/latest/catalog.html> Available maps: HapMapII_GRCh37, DeCodeSexAveraged_GRCh36, PyrhoACB_GRCh37, PyrhoASW_GRCh37, PyrhoBEB_GRCh37, PyrhoCDX_GRCh37, PyrhoCEU_GRCh37, PyrhoCHB_GRCh37, PyrhoCHS_GRCh37, PyrhoCLM_GRCh37, PyrhoESN_GRCh37, PyrhoFIN_GRCh37, PyrhoGBR_GRCh37, PyrhoGIH_GRCh37, PyrhoGWD_GRCh37, PyrhoIBS_GRCh37, PyrhoITU_GRCh37, PyrhoJPT_GRCh37, PyrhoKHV_GRCh37, PyrhoLWK_GRCh37, PyrhoMSL_GRCh37, PyrhoMXL_GRCh37, PyrhoPEL_GRCh37, PyrhoPJL_GRCh37, PyrhoPUR_GRCh37, PyrhoSTU_GRCh37, PyrhoTSI_GRCh37, PyrhoYRI_GRCh37.

-c, --chromosome

Possible choices: 1, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17, 18, chr18, 19, chr19, 20, chr20, 21, chr21, 22, chr22, X, chrX, Y, chrY, MT, chrM

Simulate a specific chromosome. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT. Default=1.

Default: “1”

-l, --length-multiplier

Simulate a sequence of length l times the named chromosome’s length, using the named chromosome’s mutation and recombination rates.

Default: 1

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

-d, --demographic-model

Possible choices: OutOfAfrica_3G09, OutOfAfrica_2T12, Africa_1T12, AmericanAdmixture_4B11, OutOfAfricaArchaicAdmixture_5R19, Zigzag_1S14, AncientEurasia_9K19, PapuansOutOfAfrica_10J19, AshkSub_7G19

Specify a simulation model. If no model is specified, a single populationconstant size model is used. Available models:OutOfAfrica_3G09, OutOfAfrica_2T12, Africa_1T12, AmericanAdmixture_4B11, OutOfAfricaArchaicAdmixture_5R19, Zigzag_1S14, AncientEurasia_9K19, PapuansOutOfAfrica_10J19, AshkSub_7G19. Please see –help-models for details of these models.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

PonAbe

Run simulations for Pongo abelii using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘–output’ option to specify a filename.

Default population parameters for Pongo abelii: Generation time: 20 Population size: 17900.0 Mutation rate: 1.4999999999999995e-08 Recombination rate: 5.64983004879663e-09

stdpopsim PonAbe [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
                 [--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g] [-c]
                 [-l LENGTH_MULTIPLIER] [-s SEED] [-d] [-o OUTPUT]
                 samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

--help-genetic-maps

Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps

-D, --dry-run

Do not run actual simulation

Default: False

-g, --genetic-map

Possible choices: NaterPA_PonAbe2, NaterPP_PonAbe2

Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://stdpopsim.readthedocs.io/en/latest/catalog.html> Available maps: NaterPA_PonAbe2, NaterPP_PonAbe2.

-c, --chromosome

Possible choices: 1, 2a, 2b, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, MT

Simulate a specific chromosome. Options: 1, 2a, 2b, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, MT. Default=1.

Default: “1”

-l, --length-multiplier

Simulate a sequence of length l times the named chromosome’s length, using the named chromosome’s mutation and recombination rates.

Default: 1

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

-d, --demographic-model

Possible choices: TwoSpecies_2L11

Specify a simulation model. If no model is specified, a single populationconstant size model is used. Available models:TwoSpecies_2L11. Please see –help-models for details of these models.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

download-genetic-maps

Download genetic maps and store them in the cache directory. Maps are downloaded regardless of whether they are already in the cache or not. Please use the –cache-dir option to download maps to a specific directory.

stdpopsim download-genetic-maps [-h]
                                [species] [genetic_maps [genetic_maps ...]]

Positional Arguments

species

Download genetic maps for this species. If not specified download all known genetic maps.

genetic_maps

If specified, download these genetic maps. If no maps are provided, download all maps for this species.