Command line interface

Command line interface#

Command line interface for tskit.

usage: python3 -m tskit [-h] [-V]
                        {info,trees,vcf,individuals,nodes,edges,sites,mutations,populations,migrations,provenances}
                        ...

Positional Arguments#

subcommand

Possible choices: info, trees, vcf, individuals, nodes, edges, sites, mutations, populations, migrations, provenances

Named Arguments#

-V, --version

show program’s version number and exit

Sub-commands#

info#

Print summary information about a tree sequence.

python3 -m tskit info [-h] [tree_sequence]

Positional Arguments#

tree_sequence

The tskit tree sequence file. If not provided, read from stdin.

trees#

Print information about trees.

python3 -m tskit trees [-h] [--precision PRECISION] [--draw] [tree_sequence]

Positional Arguments#

tree_sequence

The tskit tree sequence file. If not provided, read from stdin.

Named Arguments#

--precision, -p

The number of decimal places to print in records

Default: 6

--draw, -d

Draw the trees

Default: False

vcf#

Convert the tree sequence genotypes to VCF format.

python3 -m tskit vcf [-h] [--ploidy PLOIDY] [--contig-id CONTIG_ID]
                     [--allow-position-zero]
                     [tree_sequence]

Positional Arguments#

tree_sequence

The tskit tree sequence file. If not provided, read from stdin.

Named Arguments#

--ploidy, -P

If the tree sequence does not contain information about individuals, create them by combining adjacent samples nodes into individuals of the specified ploidy. It is an error to provide this argument if the tree sequence does contain individuals

--contig-id, -c

Specify the contig id

Default: '1'

--allow-position-zero, -0

Allow position 0 sites

Default: False

individuals#

Output individuals in tabular format.

python3 -m tskit individuals [-h] [--precision PRECISION] [tree_sequence]

Positional Arguments#

tree_sequence

The tskit tree sequence file. If not provided, read from stdin.

Named Arguments#

--precision, -p

The number of decimal places to print in records

Default: 6

nodes#

Output nodes in tabular format.

python3 -m tskit nodes [-h] [--precision PRECISION] [tree_sequence]

Positional Arguments#

tree_sequence

The tskit tree sequence file. If not provided, read from stdin.

Named Arguments#

--precision, -p

The number of decimal places to print in records

Default: 6

edges#

Output edges in tabular format.

python3 -m tskit edges [-h] [--precision PRECISION] [tree_sequence]

Positional Arguments#

tree_sequence

The tskit tree sequence file. If not provided, read from stdin.

Named Arguments#

--precision, -p

The number of decimal places to print in records

Default: 6

sites#

Output sites in tabular format.

python3 -m tskit sites [-h] [--precision PRECISION] [tree_sequence]

Positional Arguments#

tree_sequence

The tskit tree sequence file. If not provided, read from stdin.

Named Arguments#

--precision, -p

The number of decimal places to print in records

Default: 6

mutations#

Output mutations in tabular format.

python3 -m tskit mutations [-h] [--precision PRECISION] [tree_sequence]

Positional Arguments#

tree_sequence

The tskit tree sequence file. If not provided, read from stdin.

Named Arguments#

--precision, -p

The number of decimal places to print in records

Default: 6

populations#

Output population information in tabular format.

python3 -m tskit populations [-h] [tree_sequence]

Positional Arguments#

tree_sequence

The tskit tree sequence file. If not provided, read from stdin.

migrations#

Output migration information in tabular format.

python3 -m tskit migrations [-h] [--precision PRECISION] [tree_sequence]

Positional Arguments#

tree_sequence

The tskit tree sequence file. If not provided, read from stdin.

Named Arguments#

--precision, -p

The number of decimal places to print in records

Default: 6

provenances#

Output provenance information in tabular format.

python3 -m tskit provenances [-h] [-H] [tree_sequence]

Positional Arguments#

tree_sequence

The tskit tree sequence file. If not provided, read from stdin.

Named Arguments#

-H, --human

Print out the provenances in a human readable format

Default: False

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