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Aug 15, 2022
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Use clap proc macro for example program. #320

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2 changes: 1 addition & 1 deletion Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ tskit-derive = {version = "0.2.0", path = "tskit-derive", optional = true}
mbox = "0.6.0"

[dev-dependencies]
clap = "~3.2.8"
clap = {version = "~3.2.8", features = ["derive"]}
serde = {version = "1.0.118", features = ["derive"]}
serde-pickle = "1.1.0"
bincode = "1.3.1"
Expand Down
145 changes: 62 additions & 83 deletions examples/forward_simulation.rs
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
use clap::Parser;
/*
* Forward simulation without selection:
*
Expand All @@ -18,22 +19,78 @@
* and numbers of crossovers, etc.., from being entered
* on the command line.
*/
use clap::{Arg, Command};
use rand::rngs::StdRng;
use rand::Rng;
use rand::SeedableRng;
use rand_distr::{Exp, Uniform};
use tskit::TableAccess;
use tskit::TskitTypeAccess;

#[derive(clap::Parser)]
struct SimParams {
#[clap(
short = 'N',
long = "popsize",
value_parser,
default_value_t = 1000,
help = "Diploid population size. Default = 1,000"
)]
pub popsize: u32,
#[clap(
short = 'n',
long = "nsteps",
value_parser,
default_value_t = 1000,
help = "Number of birth steps to simulate. For non-overlapping generations, this is the number of generations to simulate. Default = 1,000."
)]
pub nsteps: u32,
#[clap(
short = 'x',
long = "xovers",
value_parser,
default_value_t = 0.0,
help = "Mean number of crossovers per meiosis. The number of crossovers is Poisson-distributed with this value. Default = 0.0."
)]
pub xovers: f64,
#[clap(
short = 'P',
long = "psurvival",
value_parser,
default_value_t = 0.0,
help = "Survival probability. A value of 0.0 is the Wright-Fisher model of non-overlapping generations. Values must b 0.0 <= p < 1.0. Default = 0.0."
)]
pub psurvival: f64,
#[clap(
short = 'L',
long = "genome_length",
value_parser,
default_value_t = 1e6,
help = "Genome length (continuous units). Default = 1e6."
)]
pub genome_length: f64,
#[clap(
short = 's',
long = "simplification_interval",
value_parser,
default_value_t = 100,
help = "Number of birth steps between simplifications. Default = 100."
)]
pub simplification_interval: u32,
#[clap(
short = 't',
long = "treefile",
value_parser,
default_value = "treefile.trees",
help = "Name of output file. The format is a tskit \"trees\" file. Default = \"treefile.trees\"."
)]
pub treefile: String,
#[clap(
short = 'S',
long = "seed",
value_parser,
default_value_t = 0,
help = "Random number seed. Default = 0."
)]
pub seed: u64,
}

Expand Down Expand Up @@ -64,84 +121,6 @@ impl std::fmt::Display for BadParameter {
}

impl SimParams {
fn new() -> Self {
let mut params = SimParams::default();

let matches = Command::new("forward_simulation")
.arg(
Arg::new("popsize")
.short('N')
.long("popsize")
.help("Diploid population size. Default = 1,000.")
.takes_value(true),
)
.arg(
Arg::new("nsteps")
.short('n')
.long("nsteps")
.help("Number of birth steps to simulate. For non-overlapping generations, this is the number of generations to simulate. Default = 1,000.")
.takes_value(true),
)
.arg(
Arg::new("xovers")
.short('x')
.long("xovers")
.help("Mean number of crossovers per meiosis. The number of crossovers is Poisson-distributed with this value. Default = 0.0.")
.takes_value(true),
)
.arg(
Arg::new("genome_length")
.short('L')
.long("genome_length")
.help("Genome length (continuous units). Default = 1e6.")
.takes_value(true),
)
.arg(
Arg::new("simplification_interval")
.short('s')
.long("simplify")
.help("Number of birth steps between simplifications. Default = 100.")
.takes_value(true),
)
.arg(
Arg::new("treefile")
.short('t')
.long("treefile")
.help("Name of output file. The format is a tskit \"trees\" file. Default = \"treefile.trees\".")
.takes_value(true),
)
.arg(
Arg::new("seed")
.short('S')
.long("seed")
.help("Random number seed. Default = 0.")
.takes_value(true),
)
.arg(
Arg::new("psurvival")
.short('P')
.long("psurvival")
.help("Survival probability. A value of 0.0 is the Wright-Fisher model of non-overlapping generations. Values must b 0.0 <= p < 1.0. Default = 0.0.")
.takes_value(true),
)
.get_matches();

params.popsize = matches.value_of_t("popsize").unwrap_or(params.popsize);
params.nsteps = matches.value_of_t("nsteps").unwrap_or(params.nsteps);
params.xovers = matches.value_of_t("xovers").unwrap_or(params.xovers);
params.genome_length = matches
.value_of_t("genome_length")
.unwrap_or(params.genome_length);
params.simplification_interval = matches
.value_of_t("simplification_interval")
.unwrap_or(params.simplification_interval);
params.seed = matches.value_of_t("seed").unwrap_or(params.seed);
params.psurvival = matches.value_of_t("psurvival").unwrap_or(params.psurvival);
params.treefile = matches.value_of_t("treefile").unwrap_or(params.treefile);

params
}

// NOTE: This function is incomplete.
fn validate(&self) -> Result<(), BadParameter> {
match self.psurvival.partial_cmp(&0.0) {
Expand Down Expand Up @@ -501,7 +480,7 @@ fn runsim(params: &SimParams) -> tskit::TableCollection {
}

fn main() {
let params = SimParams::new();
let params = SimParams::parse();
params.validate().unwrap();

let tables = runsim(&params);
Expand All @@ -516,14 +495,14 @@ fn main() {
#[test]
#[should_panic]
fn test_bad_genome_length() {
let mut params = SimParams::new();
let mut params = SimParams::default();
params.genome_length = -1.0;
let _tables = runsim(&params);
}

#[test]
fn test_nonoverlapping_generations() {
let mut params = SimParams::new();
let mut params = SimParams::default();
params.nsteps = 500;
params.xovers = 1e-3;
params.validate().unwrap();
Expand All @@ -532,7 +511,7 @@ fn test_nonoverlapping_generations() {

#[test]
fn test_overlapping_generations() {
let mut params = SimParams::new();
let mut params = SimParams::default();
params.nsteps = 100;
params.xovers = 1e-3;
params.psurvival = 0.25;
Expand Down