Command line interface

arginfer provides a Command Line Interface to access the Python API.

$ arginfer

or

$ python3 -m arginfer

The second command is useful when multiple versions of Python are installed or if the arginfer executable is not installed on your path.

Argument details

This is the command line interface for arginfer, a probabilistic method to infer the Ancestral Recombination Graph.

usage: arginfer [-h] [-V] {infer} ...

Positional Arguments

subcommand

Possible choices: infer

Named Arguments

-V, --version

show program's version number and exit

Sub-commands:

infer

Takes the data or the ARG in tree sequence full_ARG format and returns MCMC sampled ARGs.

arginfer infer [-h] [--tsfull TSFULL] [--input_path INPUT_PATH]
               [--haplotype_name HAPLOTYPE_NAME]
               [--ancAllele_name ANCALLELE_NAME] [--snpPos_name SNPPOS_NAME]
               [--iteration ITERATION] [--thin THIN] [--burn BURN]
               [--sample_size SAMPLE_SIZE] [--seq_length SEQ_LENGTH] [--Ne NE]
               [--recombination_rate RECOMBINATION_RATE]
               [--mutation_rate MUTATION_RATE] [--outpath OUTPATH] [-p]
               [--random-seed RANDOM_SEED] [-v] [--verify]
Named Arguments
--tsfull

an msprime .args file. If None, build an ARG from haplotype data

--input_path

The path to input data, this is the path to haplotype, ancestral allele, and snp_pos

--haplotype_name

the haplotype file name

--ancAllele_name

a txt file of ancestral allele for each snp

--snpPos_name

a txt file of SNP chrom position

--iteration, -I

the number of mcmc iterations

--thin

thining steps

--burn, -b

The burn-in

--sample_size, -n

sample size

--seq_length, -L

sequence length

--Ne

effective population size

--recombination_rate, -r

the recombination rate per site per generation

--mutation_rate, -mu

the mutation rate per site per generation

--outpath, -O

The output path

-p, --plot

plot the output

--random-seed, -s
-v, --verbose

increase output verbosity

--verify

verify the output ARG