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