Command line interface#
Command line interface for tskit.
usage: python3 -m tskit [-h] [-V]
{info,trees,upgrade,vcf,individuals,nodes,edges,sites,mutations,populations,migrations,provenances}
...
Positional Arguments#
- subcommand
Possible choices: info, trees, upgrade, 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
trees#
Print information about trees.
python3 -m tskit trees [-h] [--precision PRECISION] [--draw] tree_sequence
Positional Arguments#
- tree_sequence
The tskit tree sequence file
Named Arguments#
- --precision, -p
The number of decimal places to print in records
Default: 6
- --draw, -d
Draw the trees
Default: False
upgrade#
Upgrade legacy tree sequence files.
python3 -m tskit upgrade [-h] [--remove-duplicate-positions]
source destination
Positional Arguments#
- source
The source tskit tree sequence file in legacy format
- destination
The filename of the upgraded copy.
Named Arguments#
- --remove-duplicate-positions, -d
Remove any duplicated mutation positions in the source file.
Default: False
vcf#
Convert the tree sequence genotypes to VCF format.
python3 -m tskit vcf [-h] [--ploidy PLOIDY] [--contig-id CONTIG_ID]
tree_sequence
Positional Arguments#
- tree_sequence
The tskit tree sequence file
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”
individuals#
Output individuals in tabular format.
python3 -m tskit individuals [-h] [--precision PRECISION] tree_sequence
Positional Arguments#
- tree_sequence
The tskit tree sequence file
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
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
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
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
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
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
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
Named Arguments#
- -H, --human
Print out the provenances in a human readable format
Default: False