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/peter/.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: 8.064516129032259e-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: chr1, chr2, chr3, chr4, chr5
Simulate a specific chromosome. Options: chr1, chr2, chr3, chr4, chr5. Default=chr1.
Default: “chr1”
- -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: 4.000000000000001e-09 Recombination rate: 9.506483722244084e-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: chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chr23, chr24, chr25, chr26, chr27, chr28, chr29, chr30, chr31, chr32, chr33, chr34, chr35, chr36, chr37, chr38, chrX
Simulate a specific chromosome. Options: chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chr23, chr24, chr25, chr26, chr27, chr28, chr29, chr30, chr31, chr32, chr33, chr34, chr35, chr36, chr37, chr38, chrX. Default=chr1.
Default: “chr1”
- -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: 8.4e-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: chrX, chr2L, chr2R, chr3L, chr3R, chr4, chrY
Simulate a specific chromosome. Options: chrX, chr2L, chr2R, chr3L, chr3R, chr4, chrY. Default=chrX.
Default: “chrX”
- -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: 1.29e-08 Recombination rate: 1.203828130094258e-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
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.
- -c, --chromosome
Possible choices: chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY
Simulate a specific chromosome. Options: chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY. Default=chr1.
Default: “chr1”
- -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: 1.5e-08 Recombination rate: 5.649860818501866e-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: chr1, chr2a, chr2b, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX
Simulate a specific chromosome. Options: chr1, chr2a, chr2b, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX. Default=chr1.
Default: “chr1”
- -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 ...]
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.