--- jupytext: text_representation: extension: .md format_name: myst format_version: 0.12 jupytext_version: 1.9.1 kernelspec: display_name: Python 3 language: python name: python3 --- :::{currentmodule} tskit ::: (sec_file_formats)= # File formats (sec_tree_sequence_file_format)= ## Tree sequence file format To make tree sequence data as efficient and easy as possible to use, we store the data on file in a columnar, binary format. The format is based on the [kastore](https://pypi.org/project/kastore/) package, which is a simple key-value store for numerical data. There is a one-to-one correspondence between the tables described above and the arrays stored in these files. By convention, these files are given the `.trees` suffix (although this is not enforced in any way), and we will sometimes refer to them as ".trees" files. We also refer to them as "tree sequence files". :::{todo} Link to the documentation for kastore, and describe the arrays that are stored as well as the top-level metadata. Note that a structured listing of all the data stored in a tree sequence file can be shown using e.g. ``python -m kastore ls file.trees``. ::: ### Legacy Versions Tree sequence files are versioned. This version of tskit can read ``.trees`` files produced by earlier releases that use the same *major* file format version (see ``format/version`` in a kastore listing). Files written using the pre-kastore HDF5 format (for example, by msprime < 0.6.0 or tskit < 0.6.2) cannot be read directly. To convert such legacy files, use the ``tskit upgrade`` command from an older tskit version (< 0.6.2) to produce a modern ``.trees`` file. (sec_text_file_format)= ## Text file formats The tree sequence text file format is based on a simple whitespace delimited approach. Each table corresponds to a single file, and is composed of a number of whitespace delimited columns. The first line of each file must be a **header** giving the names of each column. Subsequent rows must contain data for each of these columns, following the usual conventions. Each table has a set of mandatory and optional columns which are described below. The columns can be provided in any order, and extra columns can be included in the file. Note, in particular, that this means that an `id` column may be present in any of these files, but it will be ignored (IDs are always determined by the position of the row in a table). The {meth}`load_text` method can be used to read tables in text format. This has been used to create the following very simple tree sequence, with four nodes, two trees, and three mutations at two sites, both on the first tree: ```{code-cell} ipython3 :tags: ["hide-input"] # TODO once https://github.com/tskit-dev/tskit/issues/1824 is solved # change the individual table to include some with blank parents / locations import io import tskit from IPython.display import SVG individuals = """\ flags location parents 0 0.5,1.2 -1,-1 0 1.0,3.4 0,-1 0 3.5,6.3 0,1 0 0.5 -1,-1 0 0.5,0.5 2,3 """ nodes = """\ is_sample individual time 1 0 0.0 1 0 0.0 0 -1 2.0 0 -1 3.0 """ edges = """\ left right parent child 0.0 7.0 2 0 0.0 7.0 2 1 7.0 10.0 3 0 7.0 10.0 3 1 """ sites = """\ position ancestral_state 2.0 AT 4.0 A """ mutations = """\ site node derived_state time parent 0 0 A 0.5 -1 1 1 A 1.0 -1 1 0 T 1.5 -1 """ migrations = """\ left right node source dest time 0.0 0.7 5 2 3 1.0 0.8 0.9 8 3 4 3.0 """ populations = """\ id metadata 0 cG9wMQ== 1 cG9wMg== """ ts = tskit.load_text( individuals=io.StringIO(individuals), nodes=io.StringIO(nodes), edges=io.StringIO(edges), sites=io.StringIO(sites), mutations=io.StringIO(mutations), # migrations=io.StringIO(migrations), # uncomment when https://github.com/tskit-dev/tskit/issues/19 fixed populations=io.StringIO(populations), strict=False ) SVG(ts.draw_svg(y_axis=True)) ``` A deletion from AT to A has occurred at position 2 on the branch leading to node 0, and two mutations have occurred at position 4 on the branch leading to node 1, first from A to T, then a back mutation to A. The genotypes of our two samples, nodes 0 and 1, are therefore AA and ATA. Note that this tree sequence also contains entries in the individual, population, and migration tables, but this is not shown plot above. (sec_individual_text_format)= ### Individual text format The individual text format must contain a `flags` column. Optionally, there may also be `location`, `parents` and `metadata` columns. See the {ref}`individual table definitions` for details on these columns. Note that there are currently no globally defined `flags`, but the column is still required; a value of `0` means that there are no flags set. The `location` and `parents` columns should be a sequence of comma-separated numeric values. They do not all have to be the same length. ```{code-cell} python :tags: ["hide-input", "output-wide-tabs"] import sys from IPython.display import display, HTML display(HTML("An example individual table:")) ts.dump_text(individuals=sys.stdout) ``` (sec_node_text_format)= ### Node text format The node text format must contain the columns `is_sample` and `time`. Optionally, there may also be `population`, `individual`, and `metadata` columns. See the {ref}`node table definitions` for details on these columns. Note that we do not have a `flags` column in the text file format, but instead use `is_sample` (which may be 0 or 1). Currently, `NODE_IS_SAMPLE` is the only flag value defined for nodes, and as more flags are defined we will allow for extra columns in the text format. ```{code-cell} ipython3 :tags: ["hide-input", "output-wide-tabs"] display(HTML("An example node table:")) ts.dump_text(nodes=sys.stdout) ``` (sec_edge_text_format)= ### Edge text format The edge text format must contain the columns `left`, `right`, `parent` and `child`. Optionally, there may also be a `metadata` column. See the {ref}`edge table definitions ` for details on these columns. ```{code-cell} ipython3 :tags: ["hide-input", "output-wide-tabs"] display(HTML("An example edge table:")) ts.dump_text(edges=sys.stdout) ``` (sec_site_text_format)= ### Site text format The site text format must contain the columns `position` and `ancestral_state`. The `metadata` column may also be optionally present. See the {ref}`site table definitions ` for details on these columns. ```{code-cell} ipython3 :tags: ["hide-input", "output-wide-tabs"] display(HTML("An example site table:")) ts.dump_text(sites=sys.stdout) ``` (sec_mutation_text_format)= ### Mutation text format The mutation text format must contain the columns `site`, `node` and `derived_state`. The `time`, `parent` and `metadata` columns may also be optionally present (but `parent` must be specified if more than one mutation occurs at the same site). If the `time` column is absent, the mutation times in the resulting tree sequence are set to {data}`tskit.UNKNOWN_TIME`, which is a numeric value that behaves like NaN. Unknown mutation times written out by {meth}`TreeSequence.dump_text` are represented in the text file by the literal string ``\"unknown\"`` in the `time` column, and {func}`tskit.load_text` treats this string as `UNKNOWN_TIME` on input. See the {ref}`mutation table definitions ` for details on these columns. ```{code-cell} ipython3 :tags: ["hide-input", "output-wide-tabs"] display(HTML("An example mutation table:")) ts.dump_text(mutations=sys.stdout) ``` (sec_migration_text_format)= ### Migration text format The migration text format must contain the columns `left`, `right`, `node`, `source`, `dest` and `time`. The `metadata` column may also be optionally present. See the {ref}`migration table definitions ` for details on these columns. ```{code-cell} ipython3 :tags: ["hide-input", "output-wide-tabs"] display(HTML("An example migration table:")) print(migrations) # fixme # ts.dump_text(migrations=sys.stdout) ``` (sec_population_text_format)= ### Population text format Population tables only have a `metadata` column, so the text format for a population table requires there to be a `metadata` column. See the {ref}`population table definitions ` for details. ```{code-cell} ipython3 :tags: ["hide-input", "output-wide-tabs"] display(HTML("An example population table:")) ts.dump_text(populations=sys.stdout) ``` The `metadata` contains base64-encoded data (in this case, the strings `pop1` and `pop2`).