Python API¶

This page provides detailed documentation for the tskit Python API.

Trees and tree sequences¶

The TreeSequence class represents a sequence of correlated trees output by a simulation. The Tree class represents a single tree in this sequence. These classes are the interfaces used to interact with the trees and mutational information stored in a tree sequence returned from a simulation. There are also methods for loading data into these objects, either from the native format using tskit.load(), or from another sources using tskit.load_text() or TableCollection.tree_sequence().

Top level-classes¶

class tskit.TreeSequence

A single tree sequence, as defined by the data model. A TreeSequence instance can be created from a set of tables using TableCollection.tree_sequence(); or loaded from a set of text files using load_text(); or, loaded from a native binary file using load().

TreeSequences are immutable. To change the data held in a particular tree sequence, first get the table information as a TableCollection instance (using dump_tables()), edit those tables using the tables api, and create a new tree sequence using TableCollection.tree_sequence().

The trees() method iterates over all trees in a tree sequence, and the variants() method iterates over all sites and their genotypes.

Fst(sample_sets, indexes=None, windows=None, mode='site', span_normalise=True)

Computes “windowed” Fst between pairs of sets of nodes from sample_sets. Operates on k = 2 sample sets at a time; please see the multi-way statistics section for details on how the sample_sets and indexes arguments are interpreted and how they interact with the dimensions of the output array. See the statistics interface section for details on windows, mode, span normalise, and return value.

For sample sets X and Y, if d(X, Y) is the divergence between X and Y, and d(X) is the diversity of X, then what is computed is

Fst = 1 - 2 * (d(X) + d(Y)) / (d(X) + 2 * d(X, Y) + d(Y))


What is computed for diversity and divergence depends on mode; see those functions for more details.

Parameters
• sample_sets (list) – A list of lists of Node IDs, specifying the groups of individuals to compute the statistic with.

• indexes (list) – A list of 2-tuples.

• windows (list) – An increasing list of breakpoints between the windows to compute the statistic in.

• mode (str) – A string giving the “type” of the statistic to be computed (defaults to “site”).

• span_normalise (bool) – Whether to divide the result by the span of the window (defaults to True).

Returns

A ndarray with shape equal to (num windows, num statistics).

Tajimas_D(sample_sets=None, windows=None, mode='site')

Computes Tajima’s D of sets of nodes from sample_sets in windows. Please see the one-way statistics section for details on how the sample_sets argument is interpreted and how it interacts with the dimensions of the output array. See the statistics interface section for details on windows, mode, and return value. Operates on k = 1 sample sets at a time. For a sample set X of n nodes, if and T is the mean number of pairwise differing sites in X and S is the number of sites segregating in X (computed with diversity and segregating sites, respectively, both not span normalised), then Tajima’s D is

D = (T - S/h) / sqrt(a*S + (b/c)*S*(S-1))
h = 1 + 1/2 + ... + 1/(n-1)
g = 1 + 1/2^2 + ... + 1/(n-1)^2
a = (n+1)/(3*(n-1)*h) - 1/h^2
b = 2*(n^2 + n + 3)/(9*n*(n-1)) - (n+2)/(h*n) + g/h^2
c = h^2 + g


What is computed for diversity and divergence depends on mode; see those functions for more details.

Parameters
• sample_sets (list) – A list of lists of Node IDs, specifying the groups of individuals to compute the statistic with.

• indexes (list) – A list of 2-tuples, or None.

• windows (list) – An increasing list of breakpoints between the windows to compute the statistic in.

• mode (str) – A string giving the “type” of the statistic to be computed (defaults to “site”).

Returns

A ndarray with shape equal to (num windows, num statistics).

Y1(sample_sets, windows=None, mode='site', span_normalise=True)

Computes the ‘Y1’ statistic within each of the sets of nodes given by sample_sets. Please see the one-way statistics section for details on how the sample_sets argument is interpreted and how it interacts with the dimensions of the output array. See the statistics interface section for details on windows, mode, span normalise, and return value. Operates on k = 1 sample set at a time.

What is computed depends on mode. Each is computed exactly as Y3, except that the average is across a randomly chosen trio of samples (a1, a2, a3) all chosen without replacement from the same sample set. See Y3 for more details.

Parameters
• sample_sets (list) – A list of lists of Node IDs, specifying the groups of individuals to compute the statistic with.

• windows (list) – An increasing list of breakpoints between the windows to compute the statistic in.

• mode (str) – A string giving the “type” of the statistic to be computed (defaults to “site”).

• span_normalise (bool) – Whether to divide the result by the span of the window (defaults to True).

Returns

A ndarray with shape equal to (num windows, num statistics).

Y2(sample_sets, indexes=None, windows=None, mode='site', span_normalise=True)

Computes the ‘Y2’ statistic between pairs of sets of nodes from sample_sets. Operates on k = 2 sample sets at a time; please see the multi-way statistics section for details on how the sample_sets and indexes arguments are interpreted and how they interact with the dimensions of the output array. See the statistics interface section for details on windows, mode, span normalise, and return value.

What is computed depends on mode. Each is computed exactly as Y3, except that the average across randomly chosen trios of samples (a, b1, b2), where a is chosen from the first sample set, and b1, b2 are chosen (without replacement) from the second sample set. See Y3 for more details.

Parameters
• sample_sets (list) – A list of lists of Node IDs, specifying the groups of individuals to compute the statistic with.

• indexes (list) – A list of 2-tuples, or None.

• windows (list) – An increasing list of breakpoints between the windows to compute the statistic in.

• mode (str) – A string giving the “type” of the statistic to be computed (defaults to “site”).

• span_normalise (bool) – Whether to divide the result by the span of the window (defaults to True).

Returns

A ndarray with shape equal to (num windows, num statistics).

Y3(sample_sets, indexes=None, windows=None, mode='site', span_normalise=True)

Computes the ‘Y’ statistic between triples of sets of nodes from sample_sets. Operates on k = 3 sample sets at a time; please see the multi-way statistics section for details on how the sample_sets and indexes arguments are interpreted and how they interact with the dimensions of the output array. See the statistics interface section for details on windows, mode, span normalise, and return value.

What is computed depends on mode. Each is an average across randomly chosen trios of samples (a, b, c), one from each sample set:

“site”

The average density of sites at which a differs from b and c, per unit of chromosome length.

“branch”

The average length of all branches that separate a from b and c (in units of time).

“node”

For each node, the average proportion of the window on which a inherits from that node but b and c do not, or vice-versa.

Parameters
• sample_sets (list) – A list of lists of Node IDs, specifying the groups of individuals to compute the statistic with.

• indexes (list) – A list of 3-tuples, or None.

• windows (list) – An increasing list of breakpoints between the windows to compute the statistic in.

• mode (str) – A string giving the “type” of the statistic to be computed (defaults to “site”).

• span_normalise (bool) – Whether to divide the result by the span of the window (defaults to True).

Returns

A ndarray with shape equal to (num windows, num statistics).

allele_frequency_spectrum(sample_sets=None, windows=None, mode='site', span_normalise=True, polarised=False)

Computes the allele frequency spectrum (AFS) in windows across the genome for with respect to the specified sample_sets. See the statistics interface section for details on sample sets, windows, mode, span normalise, polarised, and return value. and see Allele frequency spectra for examples of how to use this method.

Similar to other windowed stats, the first dimension in the returned array corresponds to windows, such that result[i] is the AFS in the ith window. The AFS in each window is a k-dimensional numpy array, where k is the number of input sample sets, such that result[i, j0, j1, ...] is the value associated with frequency j0 in sample_sets[0], j1 in sample_sets[1], etc, in window i. From here, we will assume that afs corresponds to the result in a single window, i.e., afs = result[i].

If a single sample set is specified, the allele frequency spectrum within this set is returned, such that afs[j] is the value associated with frequency j. Thus, singletons are counted in afs[1], doubletons in afs[2], and so on. The zeroth entry counts alleles or branches not seen in the samples but that are polymorphic among the rest of the samples of the tree sequence; likewise, the last entry counts alleles fixed in the sample set but polymorphic in the entire set of samples. Please see the Zeroth and final entries in the AFS for an illustration.

Warning

Please note that singletons are not counted in the initial entry in each AFS array (i.e., afs[0]), but in afs[1].

If sample_sets is None (the default), the allele frequency spectrum for all samples in the tree sequence is returned.

If more than one sample set is specified, the joint allele frequency spectrum within windows is returned. For example, if we set sample_sets = [S0, S1], then afs[1, 2] counts the number of sites that at singletons within S0 and doubletons in S1. The dimensions of the output array will be [num_windows] + [1 + len(S) for S in sample_sets].

If polarised is False (the default) the AFS will be folded, so that the counts do not depend on knowing which allele is ancestral. If folded, the frequency spectrum for a single sample set S has afs[j] = 0 for all j > len(S) / 2, so that alleles at frequency j and len(S) - j both add to the same entry. If there is more than one sample set, the returned array is “lower triangular” in a similar way.

What is computed depends on mode:

“site”

The number of sites at a given frequency within the specified sample sets for each window, per unit of sequence length. To obtain the total number of sites, set span_normalise to False.

“branch”

The total length of branches in the trees subtended by subsets of the specified sample sets, per unit of sequence length. To obtain the total, set span_normalise to False.

“node”

Not supported for this method (raises a ValueError).

Parameters
• sample_sets (list) – A list of lists of Node IDs, specifying the groups of samples to compute the joint allele frequency

• windows (list) – An increasing list of breakpoints between windows along the genome.

• mode (str) – A string giving the “type” of the statistic to be computed (defaults to “site”).

• span_normalise (bool) – Whether to divide the result by the span of the window (defaults to True).

Returns

A (k + 1) dimensional numpy array, where k is the number of sample sets specified.

aslist()

Returns the trees in this tree sequence as a list. Each tree is represented by a different instance of Tree. As such, this method is inefficient and may use a large amount of memory, and should not be used when performance is a consideration. The trees() method is the recommended way to efficiently iterate over the trees in a tree sequence.

Returns

A list of the trees in this tree sequence.

Return type

list

at(position)

Returns the tree covering the specified genomic location. The returned tree will have tree.interval[0] <= position < tree.interval[1]. See also Tree.seek().

Returns

A new instance of Tree positioned to cover the specified position.

Return type

Tree

at_index(index)

Returns the tree at the specified index. See also Tree.seek_index().

Returns

A new instance of Tree positioned at the specified index.

Return type

Tree

breakpoints(as_array=False)

Returns the breakpoints along the chromosome, including the two extreme points 0 and L. This is equivalent to

>>> iter([0] + [t.interval[1] for t in self.trees()])


By default we return an iterator over the breakpoints as Python float objects; if as_array is True we return them as a numpy array.

Note that the as_array form will be more efficient and convenient in most cases; the default iterator behaviour is mainly kept to ensure compatability with existing code.

Parameters

as_array (bool) – If True, return the breakpoints as a numpy array.

Returns

The breakpoints defined by the tree intervals along the sequence.

Return type

iter or array

delete_intervals(intervals, simplify=True, record_provenance=True)

Returns a copy of this tree sequence for which information in the specified list of genomic intervals has been deleted. Edges spanning these intervals are truncated or deleted, and sites and mutations falling within them are discarded.

Note that node IDs may change as a result of this operation, as by default simplify() is called on the returned tree sequence to remove redundant nodes. If you wish to map node IDs onto the same nodes before and after this method has been called, specify simplify=False.

See also keep_intervals().

Parameters
• intervals (array_like) – A list (start, end) pairs describing the genomic intervals to delete. Intervals must be non-overlapping and in increasing order. The list of intervals must be interpretable as a 2D numpy array with shape (N, 2), where N is the number of intervals.

• simplify (bool) – If True, return a simplified tree sequence where nodes no longer used are discarded. (Default: True).

• record_provenance (bool) – If True, add details of this operation to the provenance information of the returned tree sequence. (Default: True).

Return type

TreeSequence

delete_sites(site_ids, record_provenance=True)

Returns a copy of this tree sequence with the specified sites (and their associated mutations) entirely removed. The site IDs do not need to be in any particular order, and specifying the same ID multiple times does not have any effect (i.e., calling tree_sequence.delete_sites([0, 1, 1]) has the same effect as calling tree_sequence.delete_sites([0, 1]).

Parameters
• site_ids (list[int]) – A list of site IDs specifying the sites to remove.

• record_provenance (bool) – If True, add details of this operation to the provenance information of the returned tree sequence. (Default: True).

divergence(sample_sets, indexes=None, windows=None, mode='site', span_normalise=True)

Computes mean genetic divergence between (and within) pairs of sets of nodes from sample_sets. Operates on k = 2 sample sets at a time; please see the multi-way statistics section for details on how the sample_sets and indexes arguments are interpreted and how they interact with the dimensions of the output array. See the statistics interface section for details on windows, mode, span normalise, and return value.

As a special case, an index (j, j) will compute the diversity of sample_set[j].

What is computed depends on mode:

“site”

Mean pairwise genetic divergence: the average across distinct, randomly chosen pairs of chromosomes (one from each sample set), of the density of sites at which the two carry different alleles, per unit of chromosome length.

“branch”

Mean distance in the tree: the average across distinct, randomly chosen pairs of chromsomes (one from each sample set) and locations in the window, of the mean distance in the tree between the two samples (in units of time).

“node”

For each node, the proportion of genome on which the node is an ancestor to only one of a random pair (one from each sample set), averaged over choices of pair.

Parameters
• sample_sets (list) – A list of lists of Node IDs, specifying the groups of individuals to compute the statistic with.

• indexes (list) – A list of 2-tuples, or None.

• windows (list) – An increasing list of breakpoints between the windows to compute the statistic in.

• mode (str) – A string giving the “type” of the statistic to be computed (defaults to “site”).

• span_normalise (bool) – Whether to divide the result by the span of the window (defaults to True).

Returns

A ndarray with shape equal to (num windows, num statistics).

diversity(sample_sets=None, windows=None, mode='site', span_normalise=True)

Computes mean genetic diversity (also knowns as “Tajima’s pi”) in each of the sets of nodes from sample_sets. Please see the one-way statistics section for details on how the sample_sets argument is interpreted and how it interacts with the dimensions of the output array. See the statistics interface section for details on windows, mode, span normalise, and return value.

Note that this quantity can also be computed by the divergence method.

What is computed depends on mode:

“site”

Mean pairwise genetic diversity: the average across distinct, randomly chosen pairs of chromosomes, of the density of sites at which the two carry different alleles, per unit of chromosome length.

“branch”

Mean distance in the tree: the average across distinct, randomly chosen pairs of chromsomes and locations in the window, of the mean distance in the tree between the two samples (in units of time).

“node”

For each node, the proportion of genome on which the node is an ancestor to only one of a random pair from the sample set, averaged over choices of pair.

Parameters
• sample_sets (list) – A list of lists of Node IDs, specifying the groups of individuals to compute the statistic with.

• windows (list) – An increasing list of breakpoints between the windows to compute the statistic in.

• mode (str) – A string giving the “type” of the statistic to be computed (defaults to “site”).

• span_normalise (bool) – Whether to divide the result by the span of the window (defaults to True).

Returns

A numpy array.

dump(path, zlib_compression=False)

Writes the tree sequence to the specified file path.

Parameters
• path (str) – The file path to write the TreeSequence to.

• zlib_compression (bool) – This parameter is deprecated and ignored.

dump_tables()

A copy of the tables defining this tree sequence.

Returns

A TableCollection containing all tables underlying the tree sequence.

Return type

TableCollection

dump_text(nodes=None, edges=None, sites=None, mutations=None, individuals=None, populations=None, provenances=None, precision=6, encoding='utf8', base64_metadata=True)

Writes a text representation of the tables underlying the tree sequence to the specified connections.

If Base64 encoding is not used, then metadata will be saved directly, possibly resulting in errors reading the tables back in if metadata includes whitespace.

Parameters
• nodes (stream) – The file-like object (having a .write() method) to write the NodeTable to.

• edges (stream) – The file-like object to write the EdgeTable to.

• sites (stream) – The file-like object to write the SiteTable to.

• mutations (stream) – The file-like object to write the MutationTable to.

• individuals (stream) – The file-like object to write the IndividualTable to.

• populations (stream) – The file-like object to write the PopulationTable to.

• provenances (stream) – The file-like object to write the ProvenanceTable to.

• precision (int) – The number of digits of precision.

• encoding (string) – Encoding used for text representation.

• base64_metadata (bool) – If True, metadata is encoded using Base64 encoding; otherwise, as plain text.

edge(id_)

Returns the edge in this tree sequence with the specified ID.

Return type

Edge

edge_diffs()

Returns an iterator over all the edges that are inserted and removed to build the trees as we move from left-to-right along the tree sequence. The iterator yields a sequence of 3-tuples, (interval, edges_out, edges_in). The interval is a pair (left, right) representing the genomic interval (see Tree.interval). The edges_out value is a tuple of the edges that were just-removed to create the tree covering the interval (hence edges_out will always be empty for the first tree). The edges_in value is a tuple of edges that were just inserted to construct the tree convering the current interval. The iterator terminates after the final interval in the tree sequence (i.e. it does not report a final removal of all remaining edges); the number of iterations is thus always equal to the number of trees in the tree sequence.

Returns

An iterator over the (interval, edges_out, edges_in) tuples.

Return type

iter(tuple, tuple, tuple)

edges()

Returns an iterator over all the edges in this tree sequence. Edges are returned in the order required for a valid tree sequence. So, edges are guaranteed to be ordered such that (a) all parents with a given ID are contiguous; (b) edges are returned in non-descreasing order of parent time ago; (c) within the edges for a given parent, edges are sorted first by child ID and then by left coordinate.

Returns

An iterator over all edges.

Return type

iter(Edge)

f2(sample_sets, indexes=None, windows=None, mode='site', span_normalise=True)

Computes Patterson’s f3 statistic between two groups of nodes from sample_sets. Operates on k = 2 sample sets at a time; please see the multi-way statistics section for details on how the sample_sets and indexes arguments are interpreted and how they interact with the dimensions of the output array. See the statistics interface section for details on windows, mode, span normalise, and return value.

What is computed depends on mode. Each works exactly as f4, except the average is across randomly chosen set of four samples (a1, b1; a2, b2), with a1 and a2 both chosen (without replacement) from the first sample set and b1 and b2 chosen randomly without replacement from the second sample set. See f4 for more details.

Parameters
• sample_sets (list) – A list of lists of Node IDs, specifying the groups of individuals to compute the statistic with.

• indexes (list) – A list of 2-tuples, or None.

• windows (list) – An increasing list of breakpoints between the windows to compute the statistic in.

• mode (str) – A string giving the “type” of the statistic to be computed (defaults to “site”).

• span_normalise (bool) – Whether to divide the result by the span of the window (defaults to True).

Returns

A ndarray with shape equal to (num windows, num statistics).

f3(sample_sets, indexes=None, windows=None, mode='site', span_normalise=True)

Computes Patterson’s f3 statistic between three groups of nodes from sample_sets. Operates on k = 3 sample sets at a time; please see the multi-way statistics section for details on how the sample_sets and indexes arguments are interpreted and how they interact with the dimensions of the output array. See the statistics interface section for details on windows, mode, span normalise, and return value.

What is computed depends on mode. Each works exactly as f4, except the average is across randomly chosen set of four samples (a1, b; a2, c), with a1 and a2 both chosen (without replacement) from the first sample set. See f4 for more details.

Parameters
• sample_sets (list) – A list of lists of Node IDs, specifying the groups of individuals to compute the statistic with.

• indexes (list) – A list of 3-tuples, or None.

• windows (list) – An increasing list of breakpoints between the windows to compute the statistic in.

• mode (str) – A string giving the “type” of the statistic to be computed (defaults to “site”).

• span_normalise (bool) – Whether to divide the result by the span of the window (defaults to True).

Returns

A ndarray with shape equal to (num windows, num statistics).

f4(sample_sets, indexes=None, windows=None, mode='site', span_normalise=True)

Computes Patterson’s f4 statistic between four groups of nodes from sample_sets. Operates on k = 4 sample sets at a time; please see the multi-way statistics section for details on how the sample_sets and indexes arguments are interpreted and how they interact with the dimensions of the output array. See the statistics interface section for details on windows, mode, span normalise, and return value.

What is computed depends on mode. Each is an average across randomly chosen set of four samples (a, b; c, d), one from each sample set:

“site”

The average density of sites at which a and c agree but differs from b and d, minus the average density of sites at which a and d agree but differs from b and c, per unit of chromosome length.

“branch”

The average length of all branches that separate a and c from b and d, minus the average length of all branches that separate a and d from b and c (in units of time).

“node”

For each node, the average proportion of the window on which a and c inherit from that node but b and d do not, or vice-versa, minus the average proportion of the window on which a anc d inherit from that node but b and c do not, or vice-versa.

Parameters
• sample_sets (list) – A list of lists of Node IDs, specifying the groups of individuals to compute the statistic with.

• indexes (list) – A list of 4-tuples, or None.

• windows (list) – An increasing list of breakpoints between the windows to compute the statistic in.

• mode (str) – A string giving the “type” of the statistic to be computed (defaults to “site”).

• span_normalise (bool) – Whether to divide the result by the span of the window (defaults to True).

Returns

A ndarray with shape equal to (num windows, num statistics).

first()

Returns the first tree in this TreeSequence. To iterate over all trees in the sequence, use the trees() method.

Returns

The first tree in this tree sequence.

Return type
genealogical_nearest_neighbours(focal, sample_sets, num_threads=0)

Return the genealogical nearest neighbours (GNN) proportions for the given focal nodes, with reference to two or more sets of interest, averaged over all trees in the tree sequence.

The GNN proportions for a focal node in a single tree are given by first finding the most recent common ancestral node $$a$$ between the focal node and any other node present in the reference sets. The GNN proportion for a specific reference set, $$S$$ is the number of nodes in $$S$$ that descend from $$a$$, as a proportion of the total number of descendant nodes in any of the reference sets.

For example, consider a case with 2 sample sets, $$S_1$$ and $$S_2$$. For a given tree, $$a$$ is the node that includes at least one descendant in $$S_1$$ or $$S_2$$ (not including the focal node). If the descendants of $$a$$ include some nodes in $$S_1$$ but no nodes in $$S_2$$, then the GNN proportions for that tree will be 100% $$S_1$$ and 0% $$S_2$$, or $$[1.0, 0.0]$$.

For a given focal node, the GNN proportions returned by this function are an average of the GNNs for each tree, weighted by the genomic distance spanned by that tree.

For an precise mathematical definition of GNN, see https://doi.org/10.1101/458067

Note

The reference sets need not include all the samples, hence the most recent common ancestral node of the reference sets, $$a$$, need not be the immediate ancestor of the focal node. If the reference sets only comprise sequences from relatively distant individuals, the GNN statistic may end up as a measure of comparatively distant ancestry, even for tree sequences that contain many closely related individuals.

Warning

The interface for this method is preliminary and may be subject to backwards incompatible changes in the near future. The long-term stable API for this method will be consistent with other Statistics.

Parameters
• focal (list) – A list of $$n$$ nodes whose GNNs should be calculated.

• sample_sets (list) – A list of $$m$$ lists of node IDs.

Returns

An $$n$$ by $$m$$ array of focal nodes by GNN proportions. Every focal node corresponds to a row. The numbers in each row corresponding to the GNN proportion for each of the passed-in reference sets. Rows therefore sum to one.

Return type

numpy.ndarray

general_stat(W, f, output_dim, windows=None, polarised=False, mode=None, span_normalise=True, strict=True)

Compute a windowed statistic from weights and a summary function. See the statistics interface section for details on windows, mode, span normalise, and return value. On each tree, this propagates the weights W up the tree, so that the “weight” of each node is the sum of the weights of all samples at or below the node. Then the summary function f is applied to the weights, giving a summary for each node in each tree. How this is then aggregated depends on mode:

“site”

Adds together the total summary value across all alleles in each window.

“branch”

Adds together the summary value for each node, multiplied by the length of the branch above the node and the span of the tree.

“node”

Returns each node’s summary value added across trees and multiplied by the span of the tree.

Both the weights and the summary can be multidimensional: if W has k columns, and f takes a k-vector and returns an m-vector, then the output will be m-dimensional for each node or window (depending on “mode”).

Note

The summary function f should return zero when given both 0 and the total weight (i.e., f(0) = 0 and f(np.sum(W, axis=0)) = 0), unless strict=False. This is necessary for the statistic to be unaffected by parts of the tree sequence ancestral to none or all of the samples, respectively.

Parameters
• W (ndarray) – An array of values with one row for each sample and one column for each weight.

• f (function) – A function that takes a one-dimensional array of length equal to the number of columns of W and returns a one-dimensional array.

• output_dim (int) – The length of f’s return value.

• windows (list) – An increasing list of breakpoints between the windows to compute the statistic in.

• polarised (bool) – Whether to leave the ancestral state out of computations: see Statistics for more details.

• mode (str) – A string giving the “type” of the statistic to be computed (defaults to “site”).

• span_normalise (bool) – Whether to divide the result by the span of the window (defaults to True).

• strict (bool) – Whether to check that f(0) and f(total weight) are zero.

Returns

A ndarray with shape equal to (num windows, num statistics).

genotype_matrix(impute_missing_data=False)

Returns an $$m \times n$$ numpy array of the genotypes in this tree sequence, where $$m$$ is the number of sites and $$n$$ the number of samples. The genotypes are the indexes into the array of alleles, as described for the Variant class. The value 0 always corresponds to the ancestal state, and values > 0 represent distinct derived states.

If there is missing data present the genotypes array will contain a special value tskit.MISSING_DATA (-1) to identify these missing samples. Missing data is reported by default, but if impute_missing_data is set to to True, missing data will be imputed such that all isolated samples are assigned the ancestral state. This was the default behaviour in versions prior to 0.2.0.

Warning

This method can consume a very large amount of memory! If all genotypes are not needed at once, it is usually better to access them sequentially using the variants() iterator.

Parameters

impute_missing_data (bool) – If True, the allele assigned to any isolated samples is the ancestral state; that is, we impute missing data as the ancestral state. Default: False.

Returns

The full matrix of genotypes.

Return type

numpy.ndarray (dtype=np.int8)

haplotypes(impute_missing_data=False)

Returns an iterator over the haplotypes resulting from the trees and mutations in this tree sequence as a string. The iterator returns a total of $$n$$ strings, each of which contains $$s$$ characters ($$n$$ is the sample size returned by tskit.TreeSequence.num_samples and $$s$$ is the number of sites returned by tskit.TreeSequence.num_sites). The first string returned is the haplotype for sample 0, and so on. For a given haplotype h, the value of h[j] is the observed allelic state at site j.

See also the variants() iterator for site-centric access to sample genotypes.

This method is only supported for single-letter alleles.

As missing data cannot be represented directly in the haplotypes array, an error will be raised if missing data is present. However, if impute_missing_data set to True, missing data will be imputed such that all isolated samples are assigned the ancestral state. This was the default behaviour in versions prior to 0.2.0.

Returns

An iterator over the haplotype strings for the samples in this tree sequence.

Parameters

impute_missing_data (bool) – If True, the allele assigned to any isolated samples is the ancestral state; that is, we impute missing data as the ancestral state. Default: False.

Return type

iter

Raises

LibraryError if called on a tree sequence containing multiletter alleles.

Raises

LibraryError if missing data is present and impute_missing_data is False

individual(id_)

Returns the individual in this tree sequence with the specified ID.

Return type

Individual

individuals()

Returns an iterator over all the individuals in this tree sequence.

Returns

An iterator over all individuals.

Return type

iter(Individual)

keep_intervals(intervals, simplify=True, record_provenance=True)

Returns a copy of this tree sequence which includes only information in the specified list of genomic intervals. Edges are truncated to lie within these intervals, and sites and mutations falling outside these intervals are discarded.

Note that node IDs may change as a result of this operation, as by default simplify() is called on the returned tree sequence to remove redundant nodes. If you wish to map node IDs onto the same nodes before and after this method has been called, specify simplify=False.

See also delete_intervals().

Parameters
• intervals (array_like) – A list (start, end) pairs describing the genomic intervals to keep. Intervals must be non-overlapping and in increasing order. The list of intervals must be interpretable as a 2D numpy array with shape (N, 2), where N is the number of intervals.

• simplify (bool) – If True, return a simplified tree sequence where nodes no longer used are discarded. (Default: True).

• record_provenance (bool) – If True, add details of this operation to the provenance information of the returned tree sequence. (Default: True).

Return type

TreeSequence

last()

Returns the last tree in this TreeSequence. To iterate over all trees in the sequence, use the trees() method.

Returns

The last tree in this tree sequence.

Return type
property max_root_time

Returns time of the oldest root in any of the trees in this tree sequence. This is usually equal to np.max(ts.tables.nodes.time) but may not be since there can be nodes that are not present in any tree. Consistent with the definition of tree roots, if there are no edges in the tree sequence we return the time of the oldest sample.

Returns

The maximum time of a root in this tree sequence.

Return type

float

mean_descendants(sample_sets)

Computes for every node the mean number of samples in each of the sample_sets that descend from that node, averaged over the portions of the genome for which the node is ancestral to any sample. The output is an array, C[node, j], which reports the total span of all genomes in sample_sets[j] that inherit from node, divided by the total span of the genome on which node is an ancestor to any sample in the tree sequence.

Warning

The interface for this method is preliminary and may be subject to backwards incompatible changes in the near future. The long-term stable API for this method will be consistent with other Statistics. In particular, the normalization by proportion of the genome that node is an ancestor to anyone may not be the default behaviour in the future.

Parameters

sample_sets (list) – A list of lists of node IDs.

Returns

An array with dimensions (number of nodes in the tree sequence, number of reference sets)

migrations()

Returns an iterator over all the migrations in this tree sequence.

Migrations are returned in nondecreasing order of the time value.

Returns

An iterator over all migrations.

Return type

iter(Migration)

mutation(id_)

Returns the mutation in this tree sequence with the specified ID.

Return type

Mutation

mutations()

Returns an iterator over all the mutations in this tree sequence. Mutations are returned in order of nondecreasing site ID. See the Mutation class for details on the available fields for each mutation.

The returned iterator is equivalent to iterating over all sites and all mutations in each site, i.e.:

>>> for site in tree_sequence.sites():
>>>     for mutation in site.mutations:
>>>         yield mutation

Returns

An iterator over all mutations in this tree sequence.

Return type

iter(Mutation)

node(id_)

Returns the node in this tree sequence with the specified ID.

Return type

Node

nodes()

Returns an iterator over all the nodes in this tree sequence.

Returns

An iterator over all nodes.

Return type

iter(Node)

property num_edges

Returns the number of edges in this tree sequence.

Returns

The number of edges in this tree sequence.

Return type

int

property num_individuals

Returns the number of individuals in this tree sequence.

Returns

The number of individuals in this tree sequence.

Return type

int

property num_migrations

Returns the number of migrations in this tree sequence.

Returns

The number of migrations in this tree sequence.

Return type

int

property num_mutations

Returns the number of mutations in this tree sequence.

Returns

The number of mutations in this tree sequence.

Return type

int

property num_nodes

Returns the number of nodes in this tree sequence.

Returns

The number of nodes in this tree sequence.

Return type

int

property num_populations

Returns the number of populations in this tree sequence.

Returns

The number of populations in this tree sequence.

Return type

int

property num_provenances

Returns the number of provenances in this tree sequence.

Returns

The number of provenances in this tree sequence.

Return type

int

property num_samples

Returns the number of samples in this tree sequence. This is the number of sample nodes in each tree.

Returns

The number of sample nodes in this tree sequence.

Return type

int

property num_sites

Returns the number of sites in this tree sequence.

Returns

The number of sites in this tree sequence.

Return type

int

property num_trees

Returns the number of distinct trees in this tree sequence. This is equal to the number of trees returned by the trees() method.

Returns

The number of trees in this tree sequence.

Return type

int

pairwise_diversity(samples=None)

Returns the pairwise nucleotide site diversity, the average number of sites that differ between a randomly chosen pair of samples. If samples is specified, calculate the diversity within this set.

Deprecated since version 0.2.0: please use diversity() instead. Since version 0.2.0 the error semantics have also changed slightly. It is no longer an error when there is one sample and a tskit.LibraryError is raised when non-sample IDs are provided rather than a ValueError. It is also no longer an error to compute pairwise diversity at sites with multiple mutations.

Parameters

samples (list) – The set of samples within which we calculate the diversity. If None, calculate diversity within the entire sample.

Returns

The pairwise nucleotide site diversity.

Return type

float

population(id_)

Returns the population in this tree sequence with the specified ID.

Return type

Population

populations()

Returns an iterator over all the populations in this tree sequence.

Returns

An iterator over all populations.

Return type

iter(Population)

provenances()

Returns an iterator over all the provenances in this tree sequence.

Returns

An iterator over all provenances.

Return type

iter(Provenance)

sample_count_stat(sample_sets, f, output_dim, windows=None, polarised=False, mode=None, span_normalise=True, strict=True)

Compute a windowed statistic from sample counts and a summary function. This is a wrapper around general_stat() for the common case in which the weights are all either 1 or 0, i.e., functions of the joint allele frequency spectrum. See the statistics interface section for details on sample sets, windows, mode, span normalise, and return value. If sample_sets is a list of k sets of samples, then f should be a function that takes an argument of length k and returns a one-dimensional array. The j-th element of the argument to f will be the number of samples in sample_sets[j] that lie below the node that f is being evaluated for. See general_stat() for more details.

Here is a contrived example: suppose that A and B are two sets of samples with nA and nB elements, respectively. Passing these as sample sets will give f an argument of length two, giving the number of samples in A and B below the node in question. So, if we define

def f(x):
pA = x[0] / nA
pB = x[1] / nB
return np.array([pA * pB])


then if all sites are biallelic,

ts.sample_count_stat([A, B], f, windows="site",
polarised=False, mode="site")


would compute, for each site, the product of the derived allele frequencies in the two sample sets, in a (num sites, 1) array. If instead f returns np.array([pA, pB, pA * pB]), then the output would be a (num sites, 3) array, with the first two columns giving the allele frequencies in A and B, respectively.

Note

The summary function f should return zero when given both 0 and the sample size (i.e., f(0) = 0 and f(np.array([len(x) for x in sample_sets]) = 0). This is necessary for the statistic to be unaffected by parts of the tree sequence ancestral to none or all of the samples, respectively.

Parameters
• sample_sets (list) – A list of lists of Node IDs, specifying the groups of individuals to compute the statistic with.

• f (function) – A function that takes a one-dimensional array of length equal to the number of sample sets and returns a one-dimensional array.

• output_dim (int) – The length of f’s return value.

• windows (list) – An increasing list of breakpoints between the windows to compute the statistic in.

• polarised (bool) – Whether to leave the ancestral state out of computations: see Statistics for more details.

• mode (str) – A string giving the “type” of the statistic to be computed (defaults to “site”).

• span_normalise (bool) – Whether to divide the result by the span of the window (defaults to True).

• strict (bool) – Whether to check that f(0) and f(total weight) are zero.

Returns

A ndarray with shape equal to (num windows, num statistics).

samples(population=None, population_id=None)

Returns an array of the sample node IDs in this tree sequence. If the population parameter is specified, only return sample IDs from this population.

Parameters
• population (int) – The population of interest. If None, return all samples.

• population_id (int) – Deprecated alias for population.

Returns

A numpy array of the node IDs for the samples of interest.

Return type

numpy.ndarray (dtype=np.int32)

segregating_sites(sample_sets=None, windows=None, mode='site', span_normalise=True)

Computes the density of segregating sites for each of the sets of nodes from sample_sets, and related quantities. Please see the one-way statistics section for details on how the sample_sets argument is interpreted and how it interacts with the dimensions of the output array. See the statistics interface section for details on windows, mode, span normalise, and return value.

What is computed depends on mode. For a sample set A, computes:

“site”

The sum over sites of the number of alleles found in A at each site minus one, per unit of chromosome length. If all sites have at most two alleles, this is the density of sites that are polymorphic in A. To get the number of segregating minor alleles per window, pass span_normalise=False.

“branch”

The total length of all branches in the tree subtended by the samples in A, averaged across the window.

“node”

The proportion of the window on which the node is ancestral to some, but not all, of the samples in A.

Parameters
• sample_sets (list) – A list of lists of Node IDs, specifying the groups of individuals to compute the statistic with.

• windows (list) – An increasing list of breakpoints between the windows to compute the statistic in.

• mode (str) – A string giving the “type” of the statistic to be computed (defaults to “site”).

• span_normalise (bool) – Whether to divide the result by the span of the window (defaults to True).

Returns

A ndarray with shape equal to (num windows, num statistics).

property sequence_length

Returns the sequence length in this tree sequence. This defines the genomic scale over which tree coordinates are defined. Given a tree sequence with a sequence length $$L$$, the constituent trees will be defined over the half-closed interval $$[0, L)$$. Each tree then covers some subset of this interval — see tskit.Tree.interval for details.

Returns

The length of the sequence in this tree sequence in bases.

Return type

float

simplify(samples=None, filter_zero_mutation_sites=None, map_nodes=False, reduce_to_site_topology=False, filter_populations=True, filter_individuals=True, filter_sites=True, record_provenance=True, keep_unary=False)

Returns a simplified tree sequence that retains only the history of the nodes given in the list samples. If map_nodes is true, also return a numpy array mapping the node IDs in this tree sequence to their node IDs in the simplified tree tree sequence. If a node u is not present in the new tree sequence, the value of this mapping will be NULL (-1).

In the returned tree sequence, the node with ID 0 corresponds to samples[0], node 1 corresponds to samples[1], and so on. Besides the samples, node IDs in the returned tree sequence are then allocated sequentially in time order.

If you wish to simplify a set of tables that do not satisfy all requirements for building a TreeSequence, then use TableCollection.simplify().

If the reduce_to_site_topology parameter is True, the returned tree sequence will contain only topological information that is necessary to represent the trees that contain sites. If there are zero sites in this tree sequence, this will result in an output tree sequence with zero edges. When the number of sites is greater than zero, every tree in the output tree sequence will contain at least one site. For a given site, the topology of the tree containing that site will be identical (up to node ID remapping) to the topology of the corresponding tree in the input tree sequence.

If filter_populations, filter_individuals or filter_sites is True, any of the corresponding objects that are not referenced elsewhere are filtered out. As this is the default behaviour, it is important to realise IDs for these objects may change through simplification. By setting these parameters to False, however, the corresponding tables can be preserved without changes.

Parameters
• samples (list) – The list of nodes for which to retain information. This may be a numpy array (or array-like) object (dtype=np.int32).

• filter_zero_mutation_sites (bool) – Deprecated alias for filter_sites.

• map_nodes (bool) – If True, return a tuple containing the resulting tree sequence and a numpy array mapping node IDs in the current tree sequence to their corresponding node IDs in the returned tree sequence. If False (the default), return only the tree sequence object itself.

• reduce_to_site_topology (bool) – Whether to reduce the topology down to the trees that are present at sites. (Default: False)

• filter_populations (bool) – If True, remove any populations that are not referenced by nodes after simplification; new population IDs are allocated sequentially from zero. If False, the population table will not be altered in any way. (Default: True)

• filter_individuals (bool) – If True, remove any individuals that are not referenced by nodes after simplification; new individual IDs are allocated sequentially from zero. If False, the individual table will not be altered in any way. (Default: True)

• filter_sites (bool) – If True, remove any sites that are not referenced by mutations after simplification; new site IDs are allocated sequentially from zero. If False, the site table will not be altered in any way. (Default: True)

• record_provenance (bool) – If True, record details of this call to simplify in the returned tree sequence’s provenance information (Default: True).

• keep_unary (bool) – If True, any unary nodes (i.e. nodes with exactly one child) that exist on the path from samples to root will be preserved in the output. (Default: False)

Returns

The simplified tree sequence, or (if map_nodes is True) a tuple consisting of the simplified tree sequence and a numpy array mapping source node IDs to their corresponding IDs in the new tree sequence.

Return type

TreeSequence or a (TreeSequence, numpy.array) tuple

site(id_)

Returns the site in this tree sequence with the specified ID.

Return type

Site

sites()

Returns an iterator over all the sites in this tree sequence. Sites are returned in order of increasing ID (and also position). See the Site class for details on the available fields for each site.

Returns

An iterator over all sites.

Return type

iter(Site)

property tables

A copy of the tables underlying this tree sequence. See also dump_tables().

Warning

This propery currently returns a copy of the tables underlying a tree sequence but it may return a read-only view in the future. Thus, if the tables will subsequently be updated, please use the dump_tables() method instead as this will always return a new copy of the TableCollection.

Returns

A TableCollection containing all a copy of the tables underlying this tree sequence.

Return type

TableCollection

trait_correlation(W, windows=None, mode='site', span_normalise=True)

Computes the mean squared correlations between each of the columns of W (the “phenotypes”) and inheritance along the tree sequence. See the statistics interface section for details on windows, mode, span normalise, and return value. Operates on all samples in the tree sequence.

This is computed as squared covariance in trait_covariance, but divided by $$p (1-p)$$, where p is the proportion of samples inheriting from the allele, branch, or node in question.

What is computed depends on mode:

“site”

The sum of squared correlations between presence/absence of each allele and phenotypes, divided by length of the window (if span_normalise=True). This is computed as the trait_covariance divided by the variance of the relevant column of W and by ;math:p * (1 - p), where $$p$$ is the allele frequency.

“branch”

The sum of squared correlations between the split induced by each branch and phenotypes, multiplied by branch length, averaged across trees in the window. This is computed as the trait_covariance, divided by the variance of the column of w and by $$p * (1 - p)$$, where $$p$$ is the proportion of the samples lying below the branch.

“node”

For each node, the squared correlation between the property of inheriting from this node and phenotypes, computed as in “branch”.

Note that above we divide by the sample variance, which for a vector x of length n is np.var(x) * n / (n-1).

Parameters
• W (ndarray) – An array of values with one row for each sample and one column for each “phenotype”. Each column must have positive standard deviation.

• windows (list) – An increasing list of breakpoints between the windows to compute the statistic in.

• mode (str) – A string giving the “type” of the statistic to be computed (defaults to “site”).

• span_normalise (bool) – Whether to divide the result by the span of the window (defaults to True).

Returns

A ndarray with shape equal to (num windows, num statistics).

trait_covariance(W, windows=None, mode='site', span_normalise=True)

Computes the mean squared covariances between each of the columns of W (the “phenotypes”) and inheritance along the tree sequence. See the statistics interface section for details on windows, mode, span normalise, and return value. Operates on all samples in the tree sequence.

Concretely, if g is a binary vector that indicates inheritance from an allele, branch, or node and w is a column of W, normalised to have mean zero, then the covariance of g and w is $$\sum_i g_i w_i$$, the sum of the weights corresponding to entries of g that are 1. Since weights sum to zero, this is also equal to the sum of weights whose entries of g are 0. So, $$cov(g,w)^2 = ((\sum_i g_i w_i)^2 + (\sum_i (1-g_i) w_i)^2)/2$$.

What is computed depends on mode:

“site”

The sum of squared covariances between presence/absence of each allele and phenotypes, divided by length of the window (if span_normalise=True). This is computed as sum_a (sum(w[a])^2 / 2), where w is a column of W with the average subtracted off, and w[a] is the sum of all entries of w corresponding to samples carrying allele “a”, and the first sum is over all alleles.

“branch”

The sum of squared covariances between the split induced by each branch and phenotypes, multiplied by branch length, averaged across trees in the window. This is computed as above: a branch with total weight w[b] below b contributes (branch length) * w[b]^2 to the total value for a tree. (Since the sum of w is zero, the total weight below b and not below b are equal, canceling the factor of 2 above.)

“node”

For each node, the squared covariance between the property of inheriting from this node and phenotypes, computed as in “branch”.

Parameters
• W (ndarray) – An array of values with one row for each sample and one column for each “phenotype”.

• windows (list) – An increasing list of breakpoints between the windows to compute the statistic in.

• mode (str) – A string giving the “type” of the statistic to be computed (defaults to “site”).

• span_normalise (bool) – Whether to divide the result by the span of the window (defaults to True).

Returns

A ndarray with shape equal to (num windows, num statistics).

trait_regression(W, Z=None, windows=None, mode='site', span_normalise=True)

For each trait w (i.e., each column of W), performs the least-squares linear regression $$w ~ g + Z$$, where $$g$$ is inheritance in the tree sequence and the columns of $$Z$$ are covariates, and computes the squared coefficient of $$g$$ in this regression. See the statistics interface section for details on windows, mode, span normalise, and return value. Operates on all samples in the tree sequence.

Concretely, if g is a binary vector that indicates inheritance from an allele, branch, or node and w is a column of W, there are $$k$$ columns of $$Z$$, and the $$k+2$$-vector $$b$$ minimises $$\sum_i (w_i - b_0 - b_1 g_i - b_2 z_{2,i} - ... b_{k+2} z_{k+2,i})^2$$ then this returns the number $$b_1^2$$. If $$g$$ lies in the linear span of the columns of $$Z$$, then $$b_1$$ is set to 0. To perform the regression without covariates (only the intercept), set Z = None.

What is computed depends on mode:

“site”

Computes the sum of $$b_1^2/2$$ for each allele in the window, as above with $$g$$ indicating presence/absence of the allele, then divided by the length of the window if span_normalise=True. (For biallelic loci, this number is the same for both alleles, and so summing over each cancels the factor of two.)

“branch”

The squared coefficient b_1^2, computed for the split induced by each branch (i.e., with $$g$$ indicating inheritance from that branch), multiplied by branch length and tree span, summed over all trees in the window, and divided by the length of the window if span_normalise=True.

“node”

For each node, the squared coefficient b_1^2, computed for the property of inheriting from this node, as in “branch”.

Parameters
• W (ndarray) – An array of values with one row for each sample and one column for each “phenotype”.

• Z (ndarray) – An array of values with one row for each sample and one column for each “covariate”, or None. Columns of Z must be linearly independent.

• windows (list) – An increasing list of breakpoints between the windows to compute the statistic in.

• mode (str) – A string giving the “type” of the statistic to be computed (defaults to “site”).

• span_normalise (bool) – Whether to divide the result by the span of the window (defaults to True).

Returns

A ndarray with shape equal to (num windows, num statistics).

trees(tracked_samples=None, sample_counts=True, sample_lists=False, tracked_leaves=None, leaf_counts=None, leaf_lists=None)

Returns an iterator over the trees in this tree sequence. Each value returned in this iterator is an instance of Tree. Upon successful termination of the iterator, the tree will be in the “cleared” null state.

The sample_counts, sample_lists and tracked_samples parameters are passed to the Tree constructor, and control the options that are set in the returned tree instance.

Warning

Do not store the results of this iterator in a list! For performance reasons, the same underlying object is used for every tree returned which will most likely lead to unexpected behaviour. If you wish to obtain a list of trees in a tree sequence please use ts.aslist() instead.

Parameters
• tracked_samples (list) – The list of samples to be tracked and counted using the Tree.get_num_tracked_samples() method.

• sample_counts (bool) – If True, support constant time sample counts via the Tree.num_samples() and Tree.get_num_tracked_samples() methods.

• sample_lists (bool) – If True, provide more efficient access to the samples beneath a give node using the Tree.samples() method.

Returns

An iterator over the sparse trees in this tree sequence.

Return type

iter

variants(as_bytes=False, samples=None, impute_missing_data=False)

Returns an iterator over the variants in this tree sequence. See the Variant class for details on the fields of each returned object. By default the genotypes for the variants are numpy arrays, corresponding to indexes into the alleles array. If the as_bytes parameter is true, these allelic values are recorded directly into a bytes array.

By default, genotypes are generated for all samples. The samples parameter allows us to specify the nodes for which genotypes are generated; output order of genotypes in the returned variants corresponds to the order of the samples in this list. It is also possible to provide non-sample nodes as an argument here, if you wish to generate genotypes for (e.g.) internal nodes. However, impute_missing_data must be True in this case, as it is not possible to detect missing data for non-sample nodes.

If missing data is present at a given site, the genotypes array will contain a special value tskit.MISSING_DATA (-1) to identify these missing samples. See the Variant class for more details on how missing data is reported.

Missing data is reported by default, but if impute_missing_data is set to to True, missing data will be imputed such that all isolated samples are assigned the ancestral state. This was the default behaviour in versions prior to 0.2.0.

Note

The as_bytes parameter is kept as a compatibility option for older code. It is not the recommended way of accessing variant data, and will be deprecated in a later release. Another method will be provided to obtain the allelic states for each site directly.

Parameters
• as_bytes (bool) – If True, the genotype values will be returned as a Python bytes object. This is useful in certain situations (i.e., directly printing the genotypes) or when numpy is not available. Otherwise, genotypes are returned as a numpy array (the default).

• samples (array_like) – An array of sample IDs for which to generate genotypes, or None for all samples. Default: None.

• impute_missing_data (bool) – If True, the allele assigned to any isolated samples is the ancestral state; that is, we impute missing data as the ancestral state. Default: False.

Returns

An iterator of all variants this tree sequence.

Return type

iter(Variant)

write_fasta(output, sequence_ids=None, wrap_width=60)

Writes haplotype data for samples in FASTA format to the specified file-like object.

Default sequence_ids (i.e. the text immediately following “>”) are “tsk_{sample_number}” e.g. “tsk_0”, “tsk_1” etc. They can be set by providing a list of strings to the sequence_ids argument, which must equal the length of the number of samples. Please ensure that these are unique and compatible with fasta standards, since we do not check this. Default wrap_width for sequences is 60 characters in accordance with fasta standard outputs, but this can be specified. In order to avoid any line-wrapping of sequences, set wrap_width = 0.

Example usage:

with open("output.fasta", "w") as fasta_file:
ts.write_fasta(fasta_file)


This can also be achieved on the command line use the tskit fasta command, e.g.:

$tskit fasta example.trees > example.fasta  Parameters • output (File) – The file-like object to write the fasta output. • sequence_ids (list(str)) – A list of string names to uniquely identify each of the sequences in the fasta file. If specified, this must be a list of strings of length equal to the number of samples which are output. Note that we do not check the form of these strings in any way, so that it is possible to output bad fasta IDs (for example, by including spaces before the unique identifying part of the string). The default is to output tsk_j for the jth individual. • wrap_width (int) – This parameter specifies the number of sequence characters to include on each line in the fasta file, before wrapping to the next line for each sequence. Defaults to 60 characters in accordance with fasta standard outputs. To avoid any line-wrapping of sequences, set wrap_width = 0. Otherwise, supply any positive integer. write_vcf(output, ploidy=None, contig_id='1', individuals=None, individual_names=None, position_transform=None) Writes a VCF formatted file to the specified file-like object. If there is individual information present in the tree sequence (see Individual Table), the values for sample nodes associated with these individuals are combined into phased multiploid individuals and output. If there is no individual data present in the tree sequence, synthetic individuals are created by combining adjacent samples, and the number of samples combined is equal to the specified ploidy value (1 by default). For example, if we have a ploidy of 2 and a sample of size 6, then we will have 3 diploid samples in the output, consisting of the combined genotypes for samples [0, 1], [2, 3] and [4, 5]. If we had genotypes 011110 at a particular variant, then we would output the diploid genotypes 0|1, 1|1 and 1|0 in VCF. Each individual in the output is identified by a string; these are the VCF “sample” names. By default, these are of the form tsk_0, tsk_1 etc, up to the number of individuals, but can be manually specified using the individual_names argument. We do not check for duplicates in this array, or perform any checks to ensure that the output VCF is well-formed. The REF value in the output VCF is the ancestral allele for a site and ALT values are the remaining alleles. It is important to note, therefore, that for real data this means that the REF value for a given site may not be equal to the reference allele. We also do not check that the alleles result in a valid VCF—for example, it is possible to use the tab character as an allele, leading to a broken VCF. The position_transform argument provides a way to flexibly translate the genomic location of sites in tskit to the appropriate value in VCF. There are two fundamental differences in the way that tskit and VCF define genomic coordinates. The first is that tskit uses floating point values to encode positions, whereas VCF uses integers. Thus, if the tree sequence contains positions at non-integral locations there is an information loss incurred by translating to VCF. By default, we round the site positions to the nearest integer, such that there may be several sites with the same integer position in the output. The second difference between VCF and tskit is that VCF is defined to be a 1-based coordinate system, whereas tskit uses 0-based. However, how coordinates are transformed depends on the VCF parser, and so we do not account for this change in coordinate system by default. Example usage: with open("output.vcf", "w") as vcf_file: tree_sequence.write_vcf(vcf_file, ploidy=2)  The VCF output can also be compressed using the gzip module, if you wish: import gzip with gzip.open("output.vcf.gz", "wt") as f: ts.write_vcf(f)  However, this gzipped VCF may not be fully compatible with downstream tools such as tabix, which may require the VCF use the specialised bgzip format. A general way to convert VCF data to various formats is to pipe the text produced by tskit into bcftools, as done here: import os import subprocess read_fd, write_fd = os.pipe() write_pipe = os.fdopen(write_fd, "w") with open("output.bcf", "w") as bcf_file: proc = subprocess.Popen( ["bcftools", "view", "-O", "b"], stdin=read_fd, stdout=bcf_file) ts.write_vcf(write_pipe) write_pipe.close() os.close(read_fd) proc.wait() if proc.returncode != 0: raise RuntimeError("bcftools failed with status:", proc.returncode)  This can also be achieved on the command line use the tskit vcf command, e.g.: $ tskit vcf example.trees | bcftools view -O b > example.bcf

Parameters
• output (File) – The file-like object to write the VCF output.

• ploidy (int) – The ploidy of the individuals to be written to VCF. This sample size must be evenly divisible by ploidy.

• contig_id (str) – The value of the CHROM column in the output VCF.

• individuals (list(int)) – A list containing the individual IDs to write out to VCF. Defaults to all individuals in the tree sequence.

• individual_names (list(str)) – A list of string names to identify individual columns in the VCF. In VCF nomenclature, these are the sample IDs. If specified, this must be a list of strings of length equal to the number of individuals to be output. Note that we do not check the form of these strings in any way, so that is is possible to output malformed VCF (for example, by embedding a tab character within on of the names). The default is to output tsk_j for the jth individual.

• position_transform (callable) – A callable that transforms the site position values into integer valued coordinates suitable for VCF. The function takes a single positional parameter x and must return an integer numpy array the same dimension as x. By default, this is set to numpy.round() which will round values to the nearest integer. If the string “legacy” is provided here, the pre 0.2.0 legacy behaviour of rounding values to the nearest integer (starting from 1) and avoiding the output of identical positions by incrementing is used.

class tskit.Tree(tree_sequence, tracked_samples=None, sample_counts=True, sample_lists=False)

A single tree in a TreeSequence. Please see the Moving along a tree sequence section for information on how efficiently access trees sequentially or obtain a list of individual trees in a tree sequence.

The sample_counts and sample_lists parameters control the features that are enabled for this tree. If sample_counts is True, then it is possible to count the number of samples underneath a particular node in constant time using the num_samples() method. If sample_lists is True a more efficient algorithm is used in the Tree.samples() method.

The tracked_samples parameter can be used to efficiently count the number of samples in a given set that exist in a particular subtree using the Tree.num_tracked_samples() method. It is an error to use the tracked_samples parameter when the sample_counts flag is False.

The Tree class is a state-machine which has a state corresponding to each of the trees in the parent tree sequence. We transition between these states by using the seek functions like Tree.first(), Tree.last(), Tree.seek() and Tree.seek_index(). There is one more state, the so-called “null” or “cleared” state. This is the state that a Tree is in immediately after initialisation; it has an index of -1, and no edges. We can also enter the null state by calling Tree.next() on the last tree in a sequence, calling Tree.prev() on the first tree in a sequence or calling calling the Tree.clear() method at any time.

The high-level TreeSequence seeking and iterations methods (e.g, TreeSequence.trees()) are built on these low-level state-machine seek operations. We recommend these higher level operations for most users.

Parameters
branch_length(u)

Returns the length of the branch (in generations) joining the specified node to its parent. This is equivalent to

>>> tree.time(tree.parent(u)) - tree.time(u)


The branch length for a node that has no parent (e.g., a root) is defined as zero.

Note that this is not related to the property .length which is a deprecated alias for the genomic span covered by a tree.

Parameters

u (int) – The node of interest.

Returns

The branch length from u to its parent.

Return type

float

children(u)

Returns the children of the specified node u as a tuple of integer node IDs. If u is a leaf, return the empty tuple.

Parameters

u (int) – The node of interest.

Returns

The children of u as a tuple of integers

Return type

tuple(int)

clear()

Resets this tree back to the initial null state. Calling this method on a tree already in the null state has no effect.

copy()

Returns a deep copy of this tree. The returned tree will have identical state to this tree.

Returns

A copy of this tree.

Return type

Tree

draw(path=None, width=None, height=None, node_labels=None, node_colours=None, mutation_labels=None, mutation_colours=None, format=None, edge_colours=None, tree_height_scale=None, max_tree_height=None)

Returns a drawing of this tree.

When working in a Jupyter notebook, use the IPython.display.SVG function to display the SVG output from this function inline in the notebook:

>>> SVG(tree.draw())


The unicode format uses unicode box drawing characters to render the tree. This allows rendered trees to be printed out to the terminal:

>>> print(tree.draw(format="unicode"))
6
┏━┻━┓
┃   5
┃ ┏━┻┓
┃ ┃  4
┃ ┃ ┏┻┓
3 0 1 2


The node_labels argument allows the user to specify custom labels for nodes, or no labels at all:

>>> print(tree.draw(format="unicode", node_labels={}))
┃
┏━┻━┓
┃   ┃
┃ ┏━┻┓
┃ ┃  ┃
┃ ┃ ┏┻┓
┃ ┃ ┃ ┃


Note: in some environments such as Jupyter notebooks with Windows or Mac, users have observed that the Unicode box drawings can be misaligned. In these cases, we recommend using the SVG or ASCII display formats instead. If you have a strong preference for aligned Unicode, you can try out the solution documented here.

Parameters
• path (str) – The path to the file to write the output. If None, do not write to file.

• width (int) – The width of the image in pixels. If not specified, either defaults to the minimum size required to depict the tree (text formats) or 200 pixels.

• height (int) – The height of the image in pixels. If not specified, either defaults to the minimum size required to depict the tree (text formats) or 200 pixels.

• node_labels (map) – If specified, show custom labels for the nodes that are present in the map. Any nodes not specified in the map will not have a node label.

• node_colours (map) – If specified, show custom colours for the nodes given in the map. Any nodes not specified in the map will take the default colour; a value of None is treated as transparent and hence the node symbol is not plotted. (Only supported in the SVG format.)

• mutation_labels (map) – If specified, show custom labels for the mutations (specified by ID) that are present in the map. Any mutations not in the map will not have a label. (Showing mutations is currently only supported in the SVG format)

• mutation_colours (map) – If specified, show custom colours for the mutations given in the map (specified by ID). As for node_colours, mutations not present in the map take the default colour, and those mapping to None are not drawn. (Only supported in the SVG format.)

• format (str) – The format of the returned image. Currently supported are ‘svg’, ‘ascii’ and ‘unicode’.

• edge_colours (map) – If specified, show custom colours for the edge joining each node in the map to its parent. As for node_colours, unspecified edges take the default colour, and None values result in the edge being omitted. (Only supported in the SVG format.)

• tree_height_scale (str) – Control how height values for nodes are computed. If this is equal to "time", node heights are proportional to their time values. If this is equal to "log_time", node heights are proportional to their log(time) values. If it is equal to "rank", node heights are spaced equally according to their ranked times. For SVG output the default is ‘time’-scale whereas for text output the default is ‘rank’-scale. Time scaling is not currently supported for text output.

• max_tree_height (str,float) – The maximum tree height value in the current scaling system (see tree_height_scale). Can be either a string or a numeric value. If equal to "tree", the maximum tree height is set to be that of the oldest root in the tree. If equal to "ts" the maximum height is set to be the height of the oldest root in the tree sequence; this is useful when drawing trees from the same tree sequence as it ensures that node heights are consistent. If a numeric value, this is used as the maximum tree height by which to scale other nodes. This parameters is not currently supported for text output.

Returns

A representation of this tree in the requested format.

Return type

str

first()

Seeks to the first tree in the sequence. This can be called whether the tree is in the null state or not.

property index

Returns the index this tree occupies in the parent tree sequence. This index is zero based, so the first tree in the sequence has index 0.

Returns

The index of this tree.

Return type

int

property interval

Returns the coordinates of the genomic interval that this tree represents the history of. The interval is returned as a tuple $$(l, r)$$ and is a half-open interval such that the left coordinate is inclusive and the right coordinate is exclusive. This tree therefore applies to all genomic locations $$x$$ such that $$l \leq x < r$$.

Returns

A tuple (l, r) representing the left-most (inclusive) and right-most (exclusive) coordinates of the genomic region covered by this tree.

Return type

tuple

is_descendant(u, v)

Returns True if the specified node u is a descendant of node v and False otherwise. A node $$u$$ is a descendant of another node $$v$$ if $$v$$ is on the path from $$u$$ to root. A node is considered to be a descendant of itself, so tree.is_descendant(u, u) will be True for any valid node.

Parameters
• u (int) – The descendant node.

• v (int) – The ancestral node.

Returns

True if u is a descendant of v.

Return type

bool

Raises

ValueError – If u or v are not valid node IDs.

is_internal(u)

Returns True if the specified node is not a leaf. A node is internal if it has one or more children in the current tree.

Parameters

u (int) – The node of interest.

Returns

True if u is not a leaf node.

Return type

bool

is_leaf(u)

Returns True if the specified node is a leaf. A node $$u$$ is a leaf if it has zero children.

Parameters

u (int) – The node of interest.

Returns

True if u is a leaf node.

Return type

bool

is_sample(u)

Returns True if the specified node is a sample. A node $$u$$ is a sample if it has been marked as a sample in the parent tree sequence.

Parameters

u (int) – The node of interest.

Returns

True if u is a sample.

Return type

bool

last()

Seeks to the last tree in the sequence. This can be called whether the tree is in the null state or not.

leaves(u=None)

Returns an iterator over all the leaves in this tree that are underneath the specified node. If u is not specified, return all leaves in the tree.

Parameters

u (int) – The node of interest.

Returns

An iterator over all leaves in the subtree rooted at u.

Return type

iterator

map_mutations(genotypes, alleles)

Given observations for the samples in this tree described by the specified set of genotypes and alleles, return a parsimonious set of state transitions explaining these observations. The genotypes array is interpreted as indexes into the alleles list in the same manner as described in the TreeSequence.variants() method. Thus, if sample j carries the allele at index k, then we have genotypes[j] = k. Missing data can be specified for a sample using the value tskit.MISSING_DATA (-1). At least one non-missing observation must be provided. A maximum of 63 alleles are supported.

The current implementation uses the Fitch parsimony algorithm to determine the minimum number of state transitions required to explain the data. In this model, transitions between any of the non-missing states is equally likely.

The returned values correspond directly to the data model for describing variation at sites using mutations. See the Site Table and Mutation Table definitions for details and background.

The state reconstruction is returned as two-tuple, (ancestral_state, mutations), where ancestral_state is the allele assigned to the tree root(s) and mutations is a list of Mutation objects. For each mutation, node is the tree node at the bottom of the branch on which the transition occurred, and derived_state is the new state after this mutation. When multiple mutations are returned the parent property contains the index of the previous mutation on the path to root (see the Mutation Table for more information on the concept of mutation parents). All other attributes of the Mutation object are undefined and should not be used.

See the Parsimony section in the tutorial for examples of how to use this method.

Parameters

genotypes (array_like) – The input observations for the samples in this tree.

Returns

The inferred ancestral state and list of mutations on this tree that encode the specified observations.

Return type
mrca(u, v)

Returns the most recent common ancestor of the specified nodes.

Parameters
• u (int) – The first node.

• v (int) – The second node.

Returns

The most recent common ancestor of u and v.

Return type

int

mutations()

Returns an iterator over all the mutations in this tree. Mutations are returned in order of nondecreasing site ID. See the Mutation class for details on the available fields for each mutation.

The returned iterator is equivalent to iterating over all sites and all mutations in each site, i.e.:

>>> for site in tree.sites():
>>>     for mutation in site.mutations:
>>>         yield mutation

Returns

An iterator over all Mutation objects in this tree.

Return type

iter(Mutation)

newick(precision=14, root=None, node_labels=None)

Returns a newick encoding of this tree. If the root argument is specified, return a representation of the specified subtree, otherwise the full tree is returned. If the tree has multiple roots then seperate newick strings for each rooted subtree must be found (i.e., we do not attempt to concatenate the different trees).

By default, leaf nodes are labelled with their numerical ID + 1, and internal nodes are not labelled. Arbitrary node labels can be specified using the node_labels argument, which maps node IDs to the desired labels.

Warning

Node labels are not Newick escaped, so care must be taken to provide labels that will not break the encoding.

Parameters
• precision (int) – The numerical precision with which branch lengths are printed.

• root (int) – If specified, return the tree rooted at this node.

• node_labels (map) – If specified, show custom labels for the nodes that are present in the map. Any nodes not specified in the map will not have a node label.

Returns

A newick representation of this tree.

Return type

str

next()

Seeks to the next tree in the sequence. If the tree is in the initial null state we seek to the first tree (equivalent to calling first()). Calling next on the last tree in the sequence results in the tree being cleared back into the null initial state (equivalent to calling clear()). The return value of the function indicates whether the tree is in a non-null state, and can be used to loop over the trees:

# Iterate over the trees from left-to-right
tree = tskit.Tree(tree_sequence)
while tree.next()
# Do something with the tree.
print(tree.index)
# tree is now back in the null state.

Returns

True if the tree has been transformed into one of the trees in the sequence; False if the tree has been transformed into the null state.

Return type

bool

nodes(root=None, order='preorder')

Returns an iterator over the nodes in this tree. If the root parameter is provided, iterate over the nodes in the subtree rooted at this node. If this is None, iterate over all nodes. If the order parameter is provided, iterate over the nodes in required tree traversal order.

Parameters
• root (int) – The root of the subtree we are traversing.

• order (str) – The traversal ordering. Currently ‘preorder’, ‘inorder’, ‘postorder’ and ‘levelorder’ (‘breadthfirst’) are supported.

Returns

An iterator over the nodes in the tree in some traversal order.

Return type

iterator

property num_mutations

Returns the total number of mutations across all sites on this tree.

Returns

The total number of mutations over all sites on this tree.

Return type

int

property num_nodes

Returns the number of nodes in the TreeSequence this tree is in. Equivalent to tree.tree_sequence.num_nodes. To find the number of nodes that are reachable from all roots use len(list(tree.nodes())).

Return type

int

property num_roots

The number of roots in this tree, as defined in the roots attribute.

Requires O(number of roots) time.

Return type

int

num_samples(u=None)

Returns the number of samples in this tree underneath the specified node (including the node itself). If u is not specified return the total number of samples in the tree.

If the TreeSequence.trees() method is called with sample_counts=True this method is a constant time operation. If not, a slower traversal based algorithm is used to count the samples.

Parameters

u (int) – The node of interest.

Returns

The number of samples in the subtree rooted at u.

Return type

int

property num_sites

Returns the number of sites on this tree.

Returns

The number of sites on this tree.

Return type

int

num_tracked_samples(u=None)

Returns the number of samples in the set specified in the tracked_samples parameter of the TreeSequence.trees() method underneath the specified node. If the input node is not specified, return the total number of tracked samples in the tree.

This is a constant time operation.

Parameters

u (int) – The node of interest.

Returns

The number of samples within the set of tracked samples in the subtree rooted at u.

Return type

int

Raises

RuntimeError – if the TreeSequence.trees() method is not called with sample_counts=True.

parent(u)

Returns the parent of the specified node. Returns the NULL if u is the root or is not a node in the current tree.

Parameters

u (int) – The node of interest.

Returns

The parent of u.

Return type

int

population(u)

Returns the population associated with the specified node. Equivalent to tree.tree_sequence.node(u).population.

Parameters

u (int) – The node of interest.

Returns

The ID of the population associated with node u.

Return type

int

prev()

Seeks to the previous tree in the sequence. If the tree is in the initial null state we seek to the last tree (equivalent to calling last()). Calling prev on the first tree in the sequence results in the tree being cleared back into the null initial state (equivalent to calling clear()). The return value of the function indicates whether the tree is in a non-null state, and can be used to loop over the trees:

# Iterate over the trees from right-to-left
tree = tskit.Tree(tree_sequence)
while tree.prev()
# Do something with the tree.
print(tree.index)
# tree is now back in the null state.

Returns

True if the tree has been transformed into one of the trees in the sequence; False if the tree has been transformed into the null state.

Return type

bool

property root

The root of this tree. If the tree contains multiple roots, a ValueError is raised indicating that the roots attribute should be used instead.

Returns

The root node.

Return type

int

Raises

ValueError if this tree contains more than one root.

property roots

The list of roots in this tree. A root is defined as a unique endpoint of the paths starting at samples. We can define the set of roots as follows:

roots = set()
for u in tree_sequence.samples():
while tree.parent(u) != tskit.NULL:
u = tree.parent(u)
# roots is now the set of all roots in this tree.
assert sorted(roots) == sorted(tree.roots)


The roots of the tree are returned in a list, in no particular order.

Requires O(number of roots) time.

Returns

The list of roots in this tree.

Return type

list

property sample_size

Returns the sample size for this tree. This is the number of sample nodes in the tree.

Returns

The number of sample nodes in the tree.

Return type

int

samples(u=None)

Returns an iterator over all the samples in this tree that are underneath the specified node. If u is a sample, it is included in the returned iterator. If u is not specified, return all samples in the tree.

If the TreeSequence.trees() method is called with sample_lists=True, this method uses an efficient algorithm to find the samples. If not, a simple traversal based method is used.

Parameters

u (int) – The node of interest.

Returns

An iterator over all samples in the subtree rooted at u.

Return type

iterator

seek(position)

Sets the state to represent the tree that covers the specified position in the parent tree sequence. After a successful return of this method we have tree.interval[0] <= position < tree.interval[1].

Parameters

position (float) – The position along the sequence length to seek to.

Raises

ValueError – If 0 < position or position >= TreeSequence.sequence_length.

seek_index(index)

Sets the state to represent the tree at the specified index in the parent tree sequence. Negative indexes following the standard Python conventions are allowed, i.e., index=-1 will seek to the last tree in the sequence.

Parameters

index (int) – The tree index to seek to.

Raises

IndexError – If an index outside the acceptable range is provided.

sites()

Returns an iterator over all the sites in this tree. Sites are returned in order of increasing ID (and also position). See the Site class for details on the available fields for each site.

Returns

An iterator over all sites in this tree.

property span

Returns the genomic distance that this tree spans. This is defined as $$r - l$$, where $$(l, r)$$ is the genomic interval returned by interval.

Returns

The genomic distance covered by this tree.

Return type

float

time(u)

Returns the time of the specified node in generations. Equivalent to tree.tree_sequence.node(u).time.

Parameters

u (int) – The node of interest.

Returns

The time of u.

Return type

float

tmrca(u, v)

Returns the time of the most recent common ancestor of the specified nodes. This is equivalent to:

>>> tree.time(tree.mrca(u, v))

Parameters
• u (int) – The first node.

• v (int) – The second node.

Returns

The time of the most recent common ancestor of u and v.

Return type

float

property total_branch_length

Returns the sum of all the branch lengths in this tree (in units of generations). This is equivalent to

>>> sum(tree.branch_length(u) for u in tree.nodes())


Note that the branch lengths for root nodes are defined as zero.

As this is defined by a traversal of the tree, technically we return the sum of all branch lengths that are reachable from roots. Thus, this is the sum of all branches that are ancestral to at least one sample. This distinction is only important in tree sequences that contain ‘dead branches’, i.e., those that define topology not ancestral to any samples.

Returns

The sum of lengths of branches in this tree.

Return type

float

property tree_sequence

Returns the tree sequence that this tree is from.

Returns

The parent tree sequence for this tree.

Return type

TreeSequence

Constants¶

tskit.NULL == -1

Special reserved value representing a null ID.

tskit.FORWARD == 1

Constant representing the forward direction of travel (i.e., increasing genomic coordinate values).

tskit.REVERSE == -1

Constant representing the reverse direction of travel (i.e., decreasing genomic coordinate values).

Simple container classes¶

These classes are simple shallow containers representing the entities defined in the Definitions. These classes are not intended to be instantiated directly, but are the return types for the various iterators provided by the TreeSequence and Tree classes.

class tskit.Individual

An individual in a tree sequence. Since nodes correspond to genomes, individuals are associated with a collection of nodes (e.g., two nodes per diploid). See Nodes, Genomes, or Individuals? for more discussion of this distinction.

Modifying the attributes in this class will have no effect on the underlying tree sequence data.

Variables
• id (int) – The integer ID of this individual. Varies from 0 to TreeSequence.num_individuals - 1.

• flags (int) – The bitwise flags for this individual.

• location (numpy.ndarray) – The spatial location of this individual as a numpy array. The location is an empty array if no spatial location is defined.

• nodes – The IDs of the nodes that are associated with this individual as a numpy array (dtype=np.int32). If no nodes are associated with the individual this array will be empty.

class tskit.Node

A node in a tree sequence, corresponding to a single genome. The time and population are attributes of the Node, rather than the Individual, as discussed in Nodes, Genomes, or Individuals?.

Modifying the attributes in this class will have no effect on the underlying tree sequence data.

Variables
• id (int) – The integer ID of this node. Varies from 0 to TreeSequence.num_nodes - 1.

• flags (int) – The bitwise flags for this node.

• time (float) – The birth time of this node.

• population (int) – The integer ID of the population that this node was born in.

• individual (int) – The integer ID of the individual that this node was a part of.

is_sample()

Returns True if this node is a sample. This value is derived from the flag variable.

Return type

bool

class tskit.Edge

An edge in a tree sequence.

Modifying the attributes in this class will have no effect on the underlying tree sequence data.

Variables
• left (float) – The left coordinate of this edge.

• right (float) – The right coordinate of this edge.

• parent (int) – The integer ID of the parent node for this edge. To obtain further information about a node with a given ID, use TreeSequence.node().

• child (int) – The integer ID of the child node for this edge. To obtain further information about a node with a given ID, use TreeSequence.node().

• id (int) – The integer ID of this edge. Varies from 0 to TreeSequence.num_edges - 1.

class tskit.Site

A site in a tree sequence.

Modifying the attributes in this class will have no effect on the underlying tree sequence data.

Variables
• id (int) – The integer ID of this site. Varies from 0 to TreeSequence.num_sites - 1.

• position (float) – The floating point location of this site in genome coordinates. Ranges from 0 (inclusive) to TreeSequence.sequence_length (exclusive).

• ancestral_state (str) – The ancestral state at this site (i.e., the state inherited by nodes, unless mutations occur).

• mutations (list[Mutation]) – The list of mutations at this site. Mutations within a site are returned in the order they are specified in the underlying MutationTable.

class tskit.Mutation

A mutation in a tree sequence.

Modifying the attributes in this class will have no effect on the underlying tree sequence data.

Variables
• id (int) – The integer ID of this mutation. Varies from 0 to TreeSequence.num_mutations - 1.

• site (int) – The integer ID of the site that this mutation occurs at. To obtain further information about a site with a given ID use TreeSequence.site().

• node (int) – The integer ID of the first node that inherits this mutation. To obtain further information about a node with a given ID, use TreeSequence.node().

• derived_state (str) – The derived state for this mutation. This is the state inherited by nodes in the subtree rooted at this mutation’s node, unless another mutation occurs.

• parent (int) – The integer ID of this mutation’s parent mutation. When multiple mutations occur at a site along a path in the tree, mutations must record the mutation that is immediately above them. If the mutation does not have a parent, this is equal to the NULL (-1). To obtain further information about a mutation with a given ID, use TreeSequence.mutation().

class tskit.Variant

A variant represents the observed variation among samples for a given site. A variant consists (a) of a reference to the Site instance in question; (b) the alleles that may be observed at the samples for this site; and (c) the genotypes mapping sample IDs to the observed alleles.

Each element in the alleles tuple is a string, representing the actual observed state for a given sample. The first element of this tuple is guaranteed to be the same as the site’s ancestral_state value. The list of alleles is also guaranteed not to contain any duplicates. However, allelic values may be listed that are not referred to by any samples. For example, if we have a site that is fixed for the derived state (i.e., we have a mutation over the tree root), all genotypes will be 1, but the alleles list will be equal to ('0', '1'). Other than the ancestral state being the first allele, the alleles are listed in no particular order, and the ordering should not be relied upon (but see the notes on missing data below).

The genotypes represent the observed allelic states for each sample, such that var.alleles[var.genotypes[j]] gives the string allele for sample ID j. Thus, the elements of the genotypes array are indexes into the alleles list. The genotypes are provided in this way via a numpy array to enable efficient calculations.

When missing data is present at a given site boolean flag has_missing_data will be True, at least one element of the genotypes array will be equal to tskit.MISSING_DATA, and the last element of the alleles array will be None. Note that in this case variant.num_alleles will not be equal to len(variant.alleles). The rationale for adding None to the end of the alleles list is to help code that does not handle missing data correctly fail early rather than introducing subtle and hard-to-find bugs. As tskit.MISSING_DATA is equal to -1, code that decodes genotypes into allelic values without taking missing data into account would otherwise output the last allele in the list rather missing data.

Modifying the attributes in this class will have no effect on the underlying tree sequence data.

Variables
• site (Site) – The site object for this variant.

• alleles (tuple(str)) – A tuple of the allelic values that may be observed at the samples at the current site. The first element of this tuple is always the site’s ancestral state.

• genotypes (numpy.ndarray) – An array of indexes into the list alleles, giving the state of each sample at the current site.

• has_missing_data (bool) – True if there is missing data for any of the samples at the current site.

• num_alleles (int) – The number of distinct alleles at this site. Note that this may be greater than the number of distinct values in the genotypes array.

class tskit.Migration

A migration in a tree sequence.

Modifying the attributes in this class will have no effect on the underlying tree sequence data.

Variables
• left (float) – The left end of the genomic interval covered by this migration (inclusive).

• right (float) – The right end of the genomic interval covered by this migration (exclusive).

• node (int) – The integer ID of the node involved in this migration event. To obtain further information about a node with a given ID, use TreeSequence.node().

• source (int) – The source population ID.

• dest (int) – The destination population ID.

• time (float) – The time at which this migration occured at.

class tskit.Population

A population in a tree sequence.

Modifying the attributes in this class will have no effect on the underlying tree sequence data.

Variables
• id (int) – The integer ID of this population. Varies from 0 to TreeSequence.num_populations - 1.

There are several methods for loading data into a TreeSequence instance. The simplest and most convenient is the use the tskit.load() function to load a tree sequence file. For small scale data and debugging, it is often convenient to use the tskit.load_text() to read data in the text file format. The TableCollection.tree_sequence() function efficiently creates a TreeSequence object from a set of tables using the Tables API.

tskit.load(path)

Loads a tree sequence from the specified file path. This file must be in the tree sequence file format produced by the TreeSequence.dump() method.

Parameters

path (str) – The file path of the .trees file containing the tree sequence we wish to load.

Returns

The tree sequence object containing the information stored in the specified file path.

Return type

tskit.TreeSequence

tskit.load_text(nodes, edges, sites=None, mutations=None, individuals=None, populations=None, sequence_length=0, strict=True, encoding='utf8', base64_metadata=True)

Parses the tree sequence data from the specified file-like objects, and returns the resulting TreeSequence object. The format for these files is documented in the Text file formats section, and is produced by the TreeSequence.dump_text() method. Further properties required for an input tree sequence are described in the Valid tree sequence requirements section. This method is intended as a convenient interface for importing external data into tskit; the binary file format using by tskit.load() is many times more efficient than this text format.

The nodes and edges parameters are mandatory and must be file-like objects containing text with whitespace delimited columns, parsable by parse_nodes() and parse_edges(), respectively. sites, mutations, individuals and populations are optional, and must be parsable by parse_sites(), parse_individuals(), parse_populations(), and parse_mutations(), respectively.

TODO: there is no method to parse the remaining tables at present, so only tree sequences not requiring Population and Individual tables can be loaded. This will be fixed: https://github.com/tskit-dev/msprime/issues/498

The sequence_length parameter determines the TreeSequence.sequence_length of the returned tree sequence. If it is 0 or not specified, the value is taken to be the maximum right coordinate of the input edges. This parameter is useful in degenerate situations (such as when there are zero edges), but can usually be ignored.

The strict parameter controls the field delimiting algorithm that is used. If strict is True (the default), we require exactly one tab character separating each field. If strict is False, a more relaxed whitespace delimiting algorithm is used, such that any run of whitespace is regarded as a field separator. In most situations, strict=False is more convenient, but it can lead to error in certain situations. For example, if a deletion is encoded in the mutation table this will not be parseable when strict=False.

After parsing the tables, TableCollection.sort() is called to ensure that the loaded tables satisfy the tree sequence ordering requirements. Note that this may result in the IDs of various entities changing from their positions in the input file.

Parameters
• nodes (stream) – The file-like object containing text describing a NodeTable.

• edges (stream) – The file-like object containing text describing an EdgeTable.

• sites (stream) – The file-like object containing text describing a SiteTable.

• mutations (stream) – The file-like object containing text describing a MutationTable.

• individuals (stream) – The file-like object containing text describing a IndividualTable.

• populations (stream) – The file-like object containing text describing a PopulationTable.

• sequence_length (float) – The sequence length of the returned tree sequence. If not supplied or zero this will be inferred from the set of edges.

• strict (bool) – If True, require strict tab delimiting (default). If False, a relaxed whitespace splitting algorithm is used.

• encoding (string) – Encoding used for text representation.

• base64_metadata (bool) – If True, metadata is encoded using Base64 encoding; otherwise, as plain text.

Returns

The tree sequence object containing the information stored in the specified file paths.

Return type

tskit.TreeSequence

Tables¶

The tables API provides an efficient way of working with and interchanging tree sequence data. Each table class (e.g, NodeTable, EdgeTable) has a specific set of columns with fixed types, and a set of methods for setting and getting the data in these columns. The number of rows in the table t is given by len(t). Each table supports accessing the data either by row or column. To access the row j in table t simply use t[j]. The value returned by such an access is an instance of collections.namedtuple(), and therefore supports either positional or named attribute access. To access the data in a column, we can use standard attribute access which will return a numpy array of the data. For example:

>>> import tskit
>>> t = tskit.EdgeTable()
0
1
>>> print(t)
id      left            right           parent  child
0       0.00000000      1.00000000      10      11
1       1.00000000      2.00000000      9       11
>>> t[0]
EdgeTableRow(left=0.0, right=1.0, parent=10, child=11)
>>> t[-1]
EdgeTableRow(left=1.0, right=2.0, parent=9, child=11)
>>> t.left
array([ 0.,  1.])
>>> t.parent
array([10,  9], dtype=int32)
>>> len(t)
2
>>>


Tables also support the pickle protocol, and so can be easily serialised and deserialised (for example, when performing parallel computations using the multiprocessing module).

>>> serialised = pickle.dumps(t)
>>> print(t2)
id      left            right           parent  child
0       0.00000000      1.00000000      10      11
1       1.00000000      2.00000000      9       11


However, pickling will not be as efficient as storing tables in the native format.

Tables support the equality operator == based on the data held in the columns:

>>> t == t2
True
>>> t is t2
False
2
>>> print(t2)
id      left            right           parent  child
0       0.00000000      1.00000000      10      11
1       1.00000000      2.00000000      9       11
2       0.00000000      1.00000000      2       3
>>> t == t2
False


Text columns¶

As described in the Encoding ragged columns, working with variable length columns is somewhat more involved. Columns encoding text data store the encoded bytes of the flattened strings, and the offsets into this column in two separate arrays.

Consider the following example:

>>> t = tskit.SiteTable()
>>> print(t)
0       0.00000000      A
1       1.00000000      BB
2       2.00000000
3       3.00000000      CCC
>>> t[0]
>>> t[1]
>>> t[2]
>>> t[3]


Here we create a SiteTable and add four rows, each with a different ancestral_state. We can then access this information from each row in a straightforward manner. Working with the data in the columns is a little trickier, however:

>>> t.ancestral_state
array([65, 66, 66, 67, 67, 67], dtype=int8)
>>> t.ancestral_state_offset
array([0, 1, 3, 3, 6], dtype=uint32)
>>> tskit.unpack_strings(t.ancestral_state, t.ancestral_state_offset)
['A', 'BB', '', 'CCC']


Here, the ancestral_state array is the UTF8 encoded bytes of the flattened strings, and the ancestral_state_offset is the offset into this array for each row. The unpack_strings() function, however, is a convient way to recover the original strings from this encoding. We can also use the pack_strings() to insert data using this approach:

>>> a, off = tskit.pack_strings(["0", "12", ""])
>>> t.set_columns(position=[0, 1, 2], ancestral_state=a, ancestral_state_offset=off)
>>> print(t)
0       0.00000000      0
1       1.00000000      12
2       2.00000000


When inserting many rows with standard infinite sites mutations (i.e., ancestral state is “0”), it is more efficient to construct the numpy arrays directly than to create a list of strings and use pack_strings(). When doing this, it is important to note that it is the encoded byte values that are stored; by default, we use UTF8 (which corresponds to ASCII for simple printable characters).:

>>> t_s = tskit.SiteTable()
>>> m = 10
>>> a = ord("0") + np.zeros(m, dtype=np.int8)
>>> off = np.arange(m + 1, dtype=np.uint32)
>>> t_s.set_columns(position=np.arange(m), ancestral_state=a, ancestral_state_offset=off)
>>> print(t_s)
0       0.00000000      0
1       1.00000000      0
2       2.00000000      0
3       3.00000000      0
4       4.00000000      0
5       5.00000000      0
6       6.00000000      0
7       7.00000000      0
8       8.00000000      0
9       9.00000000      0
>>> t_s.ancestral_state
array([48, 48, 48, 48, 48, 48, 48, 48, 48, 48], dtype=int8)
>>> t_s.ancestral_state_offset
array([ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10], dtype=uint32)


Here we create 10 sites at regular positions, each with ancestral state equal to “0”. Note that we use ord("0") to get the ASCII code for “0” (48), and create 10 copies of this by adding it to an array of zeros. We have done this for illustration purposes: it is equivalent (though slower for large examples) to do a, off = tskit.pack_strings(["0"] * m).

Mutations can be handled similarly:

>>> t_m = tskit.MutationTable()
>>> site = np.arange(m, dtype=np.int32)
>>> d, off = tskit.pack_strings(["1"] * m)
>>> node = np.zeros(m, dtype=np.int32)
>>> t_m.set_columns(site=site, node=node, derived_state=d, derived_state_offset=off)
>>> print(t_m)
id      site    node    derived_state   parent  metadata
0       0       0       1       -1
1       1       0       1       -1
2       2       0       1       -1
3       3       0       1       -1
4       4       0       1       -1
5       5       0       1       -1
6       6       0       1       -1
7       7       0       1       -1
8       8       0       1       -1
9       9       0       1       -1
>>>


Binary columns¶

Columns storing binary data take the same approach as Text columns to encoding variable length data. The difference between the two is only raw bytes values are accepted: no character encoding or decoding is done on the data. Consider the following example:

>>> t = tskit.NodeTable()
b'raw bytes'
b'\x80\x03}q\x00X\x01\x00\x00\x00xq\x01G?\xf1\x99\x99\x99\x99\x99\x9as.'
{'x': 1.1}
>>> print(t)
0       0       -1      0.00000000000000        cmF3IGJ5dGVz
1       0       -1      0.00000000000000        gAN9cQBYAQAAAHhxAUc/8ZmZmZmZmnMu
array([ 114,   97,  119,   32,   98,  121,  116,  101,  115, -128,    3,
125,  113,    0,   88,    1,    0,    0,    0,  120,  113,    1,
71,   63,  -15, -103, -103, -103, -103, -103, -102,  115,   46], dtype=int8)
array([ 0,  9, 33], dtype=uint32)


Here we add two rows to a NodeTable, with different metadata. The first row contains a simple byte string, and the second contains a Python dictionary serialised using pickle. We then show several different (and seemingly incompatible!) different views on the same data.

When we access the data in a row (e.g., t[0].metadata) we are returned a Python bytes object containing precisely the bytes that were inserted. The pickled dictionary is encoded in 24 bytes containing unprintable characters, and when we unpickle it using pickle.loads(), we obtain the original dictionary.

When we print the table, however, we see some data which is seemingly unrelated to the original contents. This is because the binary data is base64 encoded to ensure that it is print-safe (and doesn’t break your terminal). (See the Metadata section for more information on the use of base64 encoding.).

Finally, when we print the metadata column, we see the raw byte values encoded as signed integers. As for Text columns, the metadata_offset column encodes the offsets into this array. So, we see that the first metadata value is 9 bytes long and the second is 24.

The pack_bytes() and unpack_bytes() functions are also useful for encoding data in these columns.

Table classes¶

This section describes the methods and variables available for each table class. For description and definition of each table’s meaning and use, see the table definitions.

class tskit.IndividualTable

A table defining the individuals in a tree sequence. Note that although each Individual has associated nodes, reference to these is not stored in the individual table, but rather reference to the individual is stored for each node in the NodeTable. This is similar to the way in which the relationship between sites and mutations is modelled.

Warning

The numpy arrays returned by table attribute accesses are copies of the underlying data. In particular, this means that you cannot edit the values in the columns by updating the attribute arrays.

NOTE: this behaviour may change in future.

Variables
• flags (numpy.ndarray, dtype=np.uint32) – The array of flags values.

• location (numpy.ndarray, dtype=np.float64) – The flattened array of floating point location values. See Encoding ragged columns for more details.

• location_offset (numpy.ndarray, dtype=np.uint32) – The array of offsets into the location column. See Encoding ragged columns for more details.

• metadata (numpy.ndarray, dtype=np.int8) – The flattened array of binary metadata values. See Binary columns for more details.

• metadata_offset (numpy.ndarray, dtype=np.uint32) – The array of offsets into the metadata column. See Binary columns for more details.

add_row(flags=0, location=None, metadata=None)

Adds a new row to this IndividualTable and returns the ID of the corresponding individual.

Parameters
• flags (int) – The bitwise flags for the new node.

• location (array-like) – A list of numeric values or one-dimensional numpy array describing the location of this individual. If not specified or None, a zero-dimensional location is stored.

• metadata (bytes) – The binary-encoded metadata for the new node. If not specified or None, a zero-length byte string is stored.

Returns

The ID of the newly added node.

Return type

int

append_columns(flags=None, location=None, location_offset=None, metadata=None, metadata_offset=None)

Appends the specified arrays to the end of the columns in this IndividualTable. This allows many new rows to be added at once.

The flags array is mandatory and defines the number of extra individuals to add to the table. The location and location_offset parameters must be supplied together, and meet the requirements for Encoding ragged columns. The metadata and metadata_offset parameters must be supplied together, and meet the requirements for Encoding ragged columns. See Binary columns for more information.

Parameters
• flags (numpy.ndarray, dtype=np.uint32) – The bitwise flags for each individual. Required.

• location (numpy.ndarray, dtype=np.float64) – The flattened location array. Must be specified along with location_offset. If not specified or None, an empty location value is stored for each individual.

• location_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the location array.

• metadata (numpy.ndarray, dtype=np.int8) – The flattened metadata array. Must be specified along with metadata_offset. If not specified or None, an empty metadata value is stored for each individual.

• metadata_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the metadata array.

asdict()

Returns a dictionary mapping the names of the columns in this table to the corresponding numpy arrays.

clear()

Deletes all rows in this table.

copy()

Returns a deep copy of this table

packset_location(locations)

Packs the specified list of location values and updates the location and location_offset columns. The length of the locations array must be equal to the number of rows in the table.

Parameters

locations (list) – A list of locations interpreted as numpy float64 arrays.

packset_metadata(metadatas)

Packs the specified list of metadata values and updates the metadata and metadata_offset columns. The length of the metadatas array must be equal to the number of rows in the table.

Parameters

set_columns(flags=None, location=None, location_offset=None, metadata=None, metadata_offset=None)

Sets the values for each column in this IndividualTable using the values in the specified arrays. Overwrites any data currently stored in the table.

The flags array is mandatory and defines the number of individuals the table will contain. The location and location_offset parameters must be supplied together, and meet the requirements for Encoding ragged columns. The metadata and metadata_offset parameters must be supplied together, and meet the requirements for Encoding ragged columns. See Binary columns for more information.

Parameters
• flags (numpy.ndarray, dtype=np.uint32) – The bitwise flags for each individual. Required.

• location (numpy.ndarray, dtype=np.float64) – The flattened location array. Must be specified along with location_offset. If not specified or None, an empty location value is stored for each individual.

• location_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the location array.

• metadata (numpy.ndarray, dtype=np.int8) – The flattened metadata array. Must be specified along with metadata_offset. If not specified or None, an empty metadata value is stored for each individual.

• metadata_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the metadata array.

truncate(num_rows)

Truncates this table so that the only the first num_rows are retained.

Parameters

num_rows (int) – The number of rows to retain in this table.

class tskit.NodeTable

A table defining the nodes in a tree sequence. See the definitions for details on the columns in this table and the tree sequence requirements section for the properties needed for a node table to be a part of a valid tree sequence.

Warning

The numpy arrays returned by table attribute accesses are copies of the underlying data. In particular, this means that you cannot edit the values in the columns by updating the attribute arrays.

NOTE: this behaviour may change in future.

Variables
• time (numpy.ndarray, dtype=np.float64) – The array of time values.

• flags (numpy.ndarray, dtype=np.uint32) – The array of flags values.

• population (numpy.ndarray, dtype=np.int32) – The array of population IDs.

• individual (numpy.ndarray, dtype=np.int32) – The array of individual IDs that each node belongs to.

• metadata (numpy.ndarray, dtype=np.int8) – The flattened array of binary metadata values. See Binary columns for more details.

• metadata_offset (numpy.ndarray, dtype=np.uint32) – The array of offsets into the metadata column. See Binary columns for more details.

add_row(flags=0, time=0, population=-1, individual=-1, metadata=None)

Adds a new row to this NodeTable and returns the ID of the corresponding node.

Parameters
• flags (int) – The bitwise flags for the new node.

• time (float) – The birth time for the new node.

• population (int) – The ID of the population in which the new node was born. Defaults to NULL.

• individual (int) – The ID of the individual in which the new node was born. Defaults to NULL.

• metadata (bytes) – The binary-encoded metadata for the new node. If not specified or None, a zero-length byte string is stored.

Returns

The ID of the newly added node.

Return type

int

append_columns(flags=None, time=None, population=None, individual=None, metadata=None, metadata_offset=None)

Appends the specified arrays to the end of the columns in this NodeTable. This allows many new rows to be added at once.

The flags, time and population arrays must all be of the same length, which is equal to the number of nodes that will be added to the table. The metadata and metadata_offset parameters must be supplied together, and meet the requirements for Encoding ragged columns. See Binary columns for more information.

Parameters
• flags (numpy.ndarray, dtype=np.uint32) – The bitwise flags for each node. Required.

• time (numpy.ndarray, dtype=np.float64) – The time values for each node. Required.

• population (numpy.ndarray, dtype=np.int32) – The population values for each node. If not specified or None, the NULL value is stored for each node.

• individual (numpy.ndarray, dtype=np.int32) – The individual values for each node. If not specified or None, the NULL value is stored for each node.

• metadata (numpy.ndarray, dtype=np.int8) – The flattened metadata array. Must be specified along with metadata_offset. If not specified or None, an empty metadata value is stored for each node.

• metadata_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the metadata array.

asdict()

Returns a dictionary mapping the names of the columns in this table to the corresponding numpy arrays.

clear()

Deletes all rows in this table.

copy()

Returns a deep copy of this table

packset_metadata(metadatas)

Packs the specified list of metadata values and updates the metadata and metadata_offset columns. The length of the metadatas array must be equal to the number of rows in the table.

Parameters

set_columns(flags=None, time=None, population=None, individual=None, metadata=None, metadata_offset=None)

Sets the values for each column in this NodeTable using the values in the specified arrays. Overwrites any data currently stored in the table.

The flags, time and population arrays must all be of the same length, which is equal to the number of nodes the table will contain. The metadata and metadata_offset parameters must be supplied together, and meet the requirements for Encoding ragged columns. See Binary columns for more information.

Parameters
• flags (numpy.ndarray, dtype=np.uint32) – The bitwise flags for each node. Required.

• time (numpy.ndarray, dtype=np.float64) – The time values for each node. Required.

• population (numpy.ndarray, dtype=np.int32) – The population values for each node. If not specified or None, the NULL value is stored for each node.

• individual (numpy.ndarray, dtype=np.int32) – The individual values for each node. If not specified or None, the NULL value is stored for each node.

• metadata (numpy.ndarray, dtype=np.int8) – The flattened metadata array. Must be specified along with metadata_offset. If not specified or None, an empty metadata value is stored for each node.

• metadata_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the metadata array.

truncate(num_rows)

Truncates this table so that the only the first num_rows are retained.

Parameters

num_rows (int) – The number of rows to retain in this table.

class tskit.EdgeTable

A table defining the edges in a tree sequence. See the definitions for details on the columns in this table and the tree sequence requirements section for the properties needed for an edge table to be a part of a valid tree sequence.

Warning

The numpy arrays returned by table attribute accesses are copies of the underlying data. In particular, this means that you cannot edit the values in the columns by updating the attribute arrays.

NOTE: this behaviour may change in future.

Variables
• left (numpy.ndarray, dtype=np.float64) – The array of left coordinates.

• right (numpy.ndarray, dtype=np.float64) – The array of right coordinates.

• parent (numpy.ndarray, dtype=np.int32) – The array of parent node IDs.

• child (numpy.ndarray, dtype=np.int32) – The array of child node IDs.

add_row(left, right, parent, child)

Adds a new row to this EdgeTable and returns the ID of the corresponding edge.

Parameters
• left (float) – The left coordinate (inclusive).

• right (float) – The right coordinate (exclusive).

• parent (int) – The ID of parent node.

• child (int) – The ID of child node.

Returns

The ID of the newly added edge.

Return type

int

append_columns(left, right, parent, child)

Appends the specified arrays to the end of the columns of this EdgeTable. This allows many new rows to be added at once.

All four parameters are mandatory, and must be numpy arrays of the same length (which is equal to the number of additional edges to add to the table).

Parameters
• left (numpy.ndarray, dtype=np.float64) – The left coordinates (inclusive).

• right (numpy.ndarray, dtype=np.float64) – The right coordinates (exclusive).

• parent (numpy.ndarray, dtype=np.int32) – The parent node IDs.

• child (numpy.ndarray, dtype=np.int32) – The child node IDs.

asdict()

Returns a dictionary mapping the names of the columns in this table to the corresponding numpy arrays.

clear()

Deletes all rows in this table.

copy()

Returns a deep copy of this table

set_columns(left=None, right=None, parent=None, child=None)

Sets the values for each column in this EdgeTable using the values in the specified arrays. Overwrites any data currently stored in the table.

All four parameters are mandatory, and must be numpy arrays of the same length (which is equal to the number of edges the table will contain).

Parameters
• left (numpy.ndarray, dtype=np.float64) – The left coordinates (inclusive).

• right (numpy.ndarray, dtype=np.float64) – The right coordinates (exclusive).

• parent (numpy.ndarray, dtype=np.int32) – The parent node IDs.

• child (numpy.ndarray, dtype=np.int32) – The child node IDs.

squash()

Sorts, then condenses the table into the smallest possible number of rows by combining any adjacent edges. A pair of edges is said to be adjacent if they have the same parent and child nodes, and if the left coordinate of one of the edges is equal to the right coordinate of the other edge. The squash method modifies an EdgeTable in place so that any set of adjacent edges is replaced by a single edge. The new edge will have the same parent and child node, a left coordinate equal to the smallest left coordinate in the set, and a right coordinate equal to the largest right coordinate in the set. The new edge table will be sorted in the canonical order (P, C, L, R).

truncate(num_rows)

Truncates this table so that the only the first num_rows are retained.

Parameters

num_rows (int) – The number of rows to retain in this table.

class tskit.MigrationTable

A table defining the migrations in a tree sequence. See the definitions for details on the columns in this table and the tree sequence requirements section for the properties needed for a migration table to be a part of a valid tree sequence.

Warning

The numpy arrays returned by table attribute accesses are copies of the underlying data. In particular, this means that you cannot edit the values in the columns by updating the attribute arrays.

NOTE: this behaviour may change in future.

Variables
• left (numpy.ndarray, dtype=np.float64) – The array of left coordinates.

• right (numpy.ndarray, dtype=np.float64) – The array of right coordinates.

• node (numpy.ndarray, dtype=np.int32) – The array of node IDs.

• source (numpy.ndarray, dtype=np.int32) – The array of source population IDs.

• dest (numpy.ndarray, dtype=np.int32) – The array of destination population IDs.

• time (numpy.ndarray, dtype=np.float64) – The array of time values.

add_row(left, right, node, source, dest, time)

Adds a new row to this MigrationTable and returns the ID of the corresponding migration.

Parameters
• left (float) – The left coordinate (inclusive).

• right (float) – The right coordinate (exclusive).

• node (int) – The node ID.

• source (int) – The ID of the source population.

• dest (int) – The ID of the destination population.

• time (float) – The time of the migration event.

Returns

The ID of the newly added migration.

Return type

int

append_columns(left, right, node, source, dest, time)

Appends the specified arrays to the end of the columns of this MigrationTable. This allows many new rows to be added at once.

All six parameters are mandatory, and must be numpy arrays of the same length (which is equal to the number of additional migrations to add to the table).

Parameters
• left (numpy.ndarray, dtype=np.float64) – The left coordinates (inclusive).

• right (numpy.ndarray, dtype=np.float64) – The right coordinates (exclusive).

• node (numpy.ndarray, dtype=np.int32) – The node IDs.

• source (numpy.ndarray, dtype=np.int32) – The source population IDs.

• dest (numpy.ndarray, dtype=np.int32) – The destination population IDs.

• time (numpy.ndarray, dtype=np.int64) – The time of each migration.

asdict()

Returns a dictionary mapping the names of the columns in this table to the corresponding numpy arrays.

clear()

Deletes all rows in this table.

copy()

Returns a deep copy of this table

set_columns(left=None, right=None, node=None, source=None, dest=None, time=None)

Sets the values for each column in this MigrationTable using the values in the specified arrays. Overwrites any data currently stored in the table.

All six parameters are mandatory, and must be numpy arrays of the same length (which is equal to the number of migrations the table will contain).

Parameters
• left (numpy.ndarray, dtype=np.float64) – The left coordinates (inclusive).

• right (numpy.ndarray, dtype=np.float64) – The right coordinates (exclusive).

• node (numpy.ndarray, dtype=np.int32) – The node IDs.

• source (numpy.ndarray, dtype=np.int32) – The source population IDs.

• dest (numpy.ndarray, dtype=np.int32) – The destination population IDs.

• time (numpy.ndarray, dtype=np.int64) – The time of each migration.

truncate(num_rows)

Truncates this table so that the only the first num_rows are retained.

Parameters

num_rows (int) – The number of rows to retain in this table.

class tskit.SiteTable

A table defining the sites in a tree sequence. See the definitions for details on the columns in this table and the tree sequence requirements section for the properties needed for a site table to be a part of a valid tree sequence.

Warning

The numpy arrays returned by table attribute accesses are copies of the underlying data. In particular, this means that you cannot edit the values in the columns by updating the attribute arrays.

NOTE: this behaviour may change in future.

Variables
• position (numpy.ndarray, dtype=np.float64) – The array of site position coordinates.

• ancestral_state (numpy.ndarray, dtype=np.int8) – The flattened array of ancestral state strings. See Text columns for more details.

• ancestral_state_offset (numpy.ndarray, dtype=np.uint32) – The offsets of rows in the ancestral_state array. See Text columns for more details.

• metadata (numpy.ndarray, dtype=np.int8) – The flattened array of binary metadata values. See Binary columns for more details.

• metadata_offset (numpy.ndarray, dtype=np.uint32) – The array of offsets into the metadata column. See Binary columns for more details.

add_row(position, ancestral_state, metadata=None)

Adds a new row to this SiteTable and returns the ID of the corresponding site.

Parameters
• position (float) – The position of this site in genome coordinates.

• ancestral_state (str) – The state of this site at the root of the tree.

• metadata (bytes) – The binary-encoded metadata for the new node. If not specified or None, a zero-length byte string is stored.

Returns

The ID of the newly added site.

Return type

int

append_columns(position, ancestral_state, ancestral_state_offset, metadata=None, metadata_offset=None)

Appends the specified arrays to the end of the columns of this SiteTable. This allows many new rows to be added at once.

The position, ancestral_state and ancestral_state_offset parameters are mandatory, and must be 1D numpy arrays. The length of the position array determines the number of additional rows to add the table. The ancestral_state and ancestral_state_offset parameters must be supplied together, and meet the requirements for Encoding ragged columns (see Text columns for more information). The metadata and metadata_offset parameters must be supplied together, and meet the requirements for Encoding ragged columns (see Binary columns for more information).

Parameters
• position (numpy.ndarray, dtype=np.float64) – The position of each site in genome coordinates.

• ancestral_state (numpy.ndarray, dtype=np.int8) – The flattened ancestral_state array. Required.

• ancestral_state_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the ancestral_state array.

• metadata (numpy.ndarray, dtype=np.int8) – The flattened metadata array. Must be specified along with metadata_offset. If not specified or None, an empty metadata value is stored for each node.

• metadata_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the metadata array.

asdict()

Returns a dictionary mapping the names of the columns in this table to the corresponding numpy arrays.

clear()

Deletes all rows in this table.

copy()

Returns a deep copy of this table

packset_ancestral_state(ancestral_states)

Packs the specified list of ancestral_state values and updates the ancestral_state and ancestral_state_offset columns. The length of the ancestral_states array must be equal to the number of rows in the table.

Parameters

ancestral_states (list(str)) – A list of string ancestral state values.

packset_metadata(metadatas)

Packs the specified list of metadata values and updates the metadata and metadata_offset columns. The length of the metadatas array must be equal to the number of rows in the table.

Parameters

set_columns(position=None, ancestral_state=None, ancestral_state_offset=None, metadata=None, metadata_offset=None)

Sets the values for each column in this SiteTable using the values in the specified arrays. Overwrites any data currently stored in the table.

The position, ancestral_state and ancestral_state_offset parameters are mandatory, and must be 1D numpy arrays. The length of the position array determines the number of rows in table. The ancestral_state and ancestral_state_offset parameters must be supplied together, and meet the requirements for Encoding ragged columns (see Text columns for more information). The metadata and metadata_offset parameters must be supplied together, and meet the requirements for Encoding ragged columns (see Binary columns for more information).

Parameters
• position (numpy.ndarray, dtype=np.float64) – The position of each site in genome coordinates.

• ancestral_state (numpy.ndarray, dtype=np.int8) – The flattened ancestral_state array. Required.

• ancestral_state_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the ancestral_state array.

• metadata (numpy.ndarray, dtype=np.int8) – The flattened metadata array. Must be specified along with metadata_offset. If not specified or None, an empty metadata value is stored for each node.

• metadata_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the metadata array.

truncate(num_rows)

Truncates this table so that the only the first num_rows are retained.

Parameters

num_rows (int) – The number of rows to retain in this table.

class tskit.MutationTable

A table defining the mutations in a tree sequence. See the definitions for details on the columns in this table and the tree sequence requirements section for the properties needed for a mutation table to be a part of a valid tree sequence.

Warning

The numpy arrays returned by table attribute accesses are copies of the underlying data. In particular, this means that you cannot edit the values in the columns by updating the attribute arrays.

NOTE: this behaviour may change in future.

Variables
• site (numpy.ndarray, dtype=np.int32) – The array of site IDs.

• node (numpy.ndarray, dtype=np.int32) – The array of node IDs.

• derived_state (numpy.ndarray, dtype=np.int8) – The flattened array of derived state strings. See Text columns for more details.

• derived_state_offset (numpy.ndarray, dtype=np.uint32) – The offsets of rows in the derived_state array. See Text columns for more details.

• parent (numpy.ndarray, dtype=np.int32) – The array of parent mutation IDs.

• metadata (numpy.ndarray, dtype=np.int8) – The flattened array of binary metadata values. See Binary columns for more details.

• metadata_offset (numpy.ndarray, dtype=np.uint32) – The array of offsets into the metadata column. See Binary columns for more details.

add_row(site, node, derived_state, parent=-1, metadata=None)

Adds a new row to this MutationTable and returns the ID of the corresponding mutation.

Parameters
• site (int) – The ID of the site that this mutation occurs at.

• node (int) – The ID of the first node inheriting this mutation.

• derived_state (str) – The state of the site at this mutation’s node.

• parent (int) – The ID of the parent mutation. If not specified, defaults to NULL.

• metadata (bytes) – The binary-encoded metadata for the new node. If not specified or None, a zero-length byte string is stored.

Returns

The ID of the newly added mutation.

Return type

int

append_columns(site, node, derived_state, derived_state_offset, parent=None, metadata=None, metadata_offset=None)

Appends the specified arrays to the end of the columns of this MutationTable. This allows many new rows to be added at once.

The site, node, derived_state and derived_state_offset parameters are mandatory, and must be 1D numpy arrays. The site and node (also parent, if supplied) arrays must be of equal length, and determine the number of additional rows to add to the table. The derived_state and derived_state_offset parameters must be supplied together, and meet the requirements for Encoding ragged columns (see Text columns for more information). The metadata and metadata_offset parameters must be supplied together, and meet the requirements for Encoding ragged columns (see Binary columns for more information).

Parameters
• site (numpy.ndarray, dtype=np.int32) – The ID of the site each mutation occurs at.

• node (numpy.ndarray, dtype=np.int32) – The ID of the node each mutation is associated with.

• derived_state (numpy.ndarray, dtype=np.int8) – The flattened derived_state array. Required.

• derived_state_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the derived_state array.

• parent (numpy.ndarray, dtype=np.int32) – The ID of the parent mutation for each mutation.

• metadata (numpy.ndarray, dtype=np.int8) – The flattened metadata array. Must be specified along with metadata_offset. If not specified or None, an empty metadata value is stored for each node.

• metadata_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the metadata array.

asdict()

Returns a dictionary mapping the names of the columns in this table to the corresponding numpy arrays.

clear()

Deletes all rows in this table.

copy()

Returns a deep copy of this table

packset_derived_state(derived_states)

Packs the specified list of derived_state values and updates the derived_state and derived_state_offset columns. The length of the derived_states array must be equal to the number of rows in the table.

Parameters

derived_states (list(str)) – A list of string derived state values.

packset_metadata(metadatas)

Packs the specified list of metadata values and updates the metadata and metadata_offset columns. The length of the metadatas array must be equal to the number of rows in the table.

Parameters

set_columns(site=None, node=None, derived_state=None, derived_state_offset=None, parent=None, metadata=None, metadata_offset=None)

Sets the values for each column in this MutationTable using the values in the specified arrays. Overwrites any data currently stored in the table.

The site, node, derived_state and derived_state_offset parameters are mandatory, and must be 1D numpy arrays. The site and node (also parent, if supplied) arrays must be of equal length, and determine the number of rows in the table. The derived_state and derived_state_offset parameters must be supplied together, and meet the requirements for Encoding ragged columns (see Text columns for more information). The metadata and metadata_offset parameters must be supplied together, and meet the requirements for Encoding ragged columns (see Binary columns for more information).

Parameters
• site (numpy.ndarray, dtype=np.int32) – The ID of the site each mutation occurs at.

• node (numpy.ndarray, dtype=np.int32) – The ID of the node each mutation is associated with.

• derived_state (numpy.ndarray, dtype=np.int8) – The flattened derived_state array. Required.

• derived_state_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the derived_state array.

• parent (numpy.ndarray, dtype=np.int32) – The ID of the parent mutation for each mutation.

• metadata (numpy.ndarray, dtype=np.int8) – The flattened metadata array. Must be specified along with metadata_offset. If not specified or None, an empty metadata value is stored for each node.

• metadata_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the metadata array.

truncate(num_rows)

Truncates this table so that the only the first num_rows are retained.

Parameters

num_rows (int) – The number of rows to retain in this table.

class tskit.PopulationTable

A table defining the populations referred to in a tree sequence. The PopulationTable stores metadata for populations that may be referred to in the NodeTable and MigrationTable”. Note that although nodes may be associated with populations, this association is stored in the NodeTable: only metadata on each population is stored in the population table.

Warning

The numpy arrays returned by table attribute accesses are copies of the underlying data. In particular, this means that you cannot edit the values in the columns by updating the attribute arrays.

NOTE: this behaviour may change in future.

Variables
• metadata (numpy.ndarray, dtype=np.int8) – The flattened array of binary metadata values. See Binary columns for more details.

• metadata_offset (numpy.ndarray, dtype=np.uint32) – The array of offsets into the metadata column. See Binary columns for more details.

add_row(metadata=None)

Adds a new row to this PopulationTable and returns the ID of the corresponding population.

Parameters

metadata (bytes) – The binary-encoded metadata for the new population. If not specified or None, a zero-length byte string is stored.

Returns

The ID of the newly added population.

Return type

int

asdict()

Returns a dictionary mapping the names of the columns in this table to the corresponding numpy arrays.

clear()

Deletes all rows in this table.

copy()

Returns a deep copy of this table

packset_metadata(metadatas)

Packs the specified list of metadata values and updates the metadata and metadata_offset columns. The length of the metadatas array must be equal to the number of rows in the table.

Parameters

set_columns(metadata=None, metadata_offset=None)

Sets the values for each column in this Table using values provided in numpy arrays. Overwrites any data currently stored in the table.

truncate(num_rows)

Truncates this table so that the only the first num_rows are retained.

Parameters

num_rows (int) – The number of rows to retain in this table.

class tskit.ProvenanceTable

A table recording the provenance (i.e., history) of this table, so that the origin of the underlying data and sequence of subsequent operations can be traced. Each row contains a “record” string (recommended format: JSON) and a timestamp.

Todo

The format of the record field will be more precisely specified in the future.

Variables
• record (numpy.ndarray, dtype=np.int8) – The flattened array containing the record strings. Text columns for more details.

• record_offset (numpy.ndarray, dtype=np.uint32) – The array of offsets into the record column. See Text columns for more details.

• timestamp (numpy.ndarray, dtype=np.int8) – The flattened array containing the timestamp strings. Text columns for more details.

• timestamp_offset (numpy.ndarray, dtype=np.uint32) – The array of offsets into the timestamp column. See Text columns for more details.

add_row(record, timestamp=None)

Adds a new row to this ProvenanceTable consisting of the specified record and timestamp. If timestamp is not specified, it is automatically generated from the current time.

Parameters
• record (str) – A provenance record, describing the parameters and environment used to generate the current set of tables.

• timestamp (str) – A string timestamp. This should be in ISO8601 form.

asdict()

Returns a dictionary mapping the names of the columns in this table to the corresponding numpy arrays.

clear()

Deletes all rows in this table.

copy()

Returns a deep copy of this table

packset_record(records)

Packs the specified list of record values and updates the record and record_offset columns. The length of the records array must be equal to the number of rows in the table.

Parameters

records (list(str)) – A list of string record values.

packset_timestamp(timestamps)

Packs the specified list of timestamp values and updates the timestamp and timestamp_offset columns. The length of the timestamps array must be equal to the number of rows in the table.

Parameters

timestamps (list(str)) – A list of string timestamp values.

set_columns(timestamp=None, timestamp_offset=None, record=None, record_offset=None)

Sets the values for each column in this Table using values provided in numpy arrays. Overwrites any data currently stored in the table.

truncate(num_rows)

Truncates this table so that the only the first num_rows are retained.

Parameters

num_rows (int) – The number of rows to retain in this table.

Table Collections¶

Each of the table classes defines a different aspect of the structure of a tree sequence. It is convenient to be able to refer to a set of these tables which together define a tree sequence. We refer to this grouping of related tables as a TableCollection. The TableCollection and TreeSequence classes are deeply related. A TreeSequence instance is based on the information encoded in a TableCollection. Tree sequences are immutable, and provide methods for obtaining trees from the sequence. A TableCollection is mutable, and does not have any methods for obtaining trees. The TableCollection class essentially exists to allow the dynamic creation of tree sequences.

class tskit.TableCollection(sequence_length=0)

A collection of mutable tables defining a tree sequence. See the Data model section for definition on the various tables and how they together define a TreeSequence. Arbitrary data can be stored in a TableCollection, but there are certain requirements that must be satisfied for these tables to be interpreted as a tree sequence.

To obtain an immutable TreeSequence instance corresponding to the current state of a TableCollection, please use the tree_sequence() method.

Variables
• individuals (IndividualTable) – The individual table.

• nodes (NodeTable) – The node table.

• edges (EdgeTable) – The edge table.

• migrations (MigrationTable) – The migration table.

• sites (SiteTable) – The site table.

• mutations (MutationTable) – The mutation table.

• populations (PopulationTable) – The population table.

• provenances (ProvenanceTable) – The provenance table.

• sequence_length (float) – The sequence length defining the coordinate space.

• file_uuid (str) – The UUID for the file this TableCollection is derived from, or None if not derived from a file.

asdict()

Returns a dictionary representation of this TableCollection.

Note: the semantics of this method changed at tskit 1.0.0. Previously a map of table names to the tables themselves was returned.

build_index()

Builds an index on this TableCollection. Any existing indexes are automatically dropped.

compute_mutation_parents()

Modifies the tables in place, computing the parent column of the mutation table. For this to work, the node and edge tables must be valid, and the site and mutation tables must be sorted (see TableCollection.sort()). This will produce an error if mutations are not sorted (i.e., if a mutation appears before its mutation parent) unless the two mutations occur on the same branch, in which case there is no way to detect the error.

The parent of a given mutation is the ID of the next mutation encountered traversing the tree upwards from that mutation, or NULL if there is no such mutation.

Note

note: This method does not check that all mutations result in a change of state, as required; see Mutation requirements.

copy()

Returns a deep copy of this TableCollection.

Returns

A deep copy of this TableCollection.

Return type

TableCollection

deduplicate_sites()

Modifies the tables in place, removing entries in the site table with duplicate position (and keeping only the first entry for each site), and renumbering the site column of the mutation table appropriately. This requires the site table to be sorted by position.

delete_intervals(intervals, simplify=True, record_provenance=True)

Delete all information from this set of tables which lies within the specified list of genomic intervals. This is identical to TreeSequence.delete_intervals() but acts in place to alter the data in this TableCollection.

Parameters
• intervals (array_like) – A list (start, end) pairs describing the genomic intervals to delete. Intervals must be non-overlapping and in increasing order. The list of intervals must be interpretable as a 2D numpy array with shape (N, 2), where N is the number of intervals.

• simplify (bool) – If True, run simplify on the tables so that nodes no longer used are discarded. (Default: True).

• record_provenance (bool) – If True, add details of this operation to the provenance table in this TableCollection. (Default: True).

delete_sites(site_ids, record_provenance=True)

Remove the specified sites entirely from the sites and mutations tables in this collection. This is identical to TreeSequence.delete_sites() but acts in place to alter the data in this TableCollection.

Parameters
• site_ids (list[int]) – A list of site IDs specifying the sites to remove.

• record_provenance (bool) – If True, add details of this operation to the provenance table in this TableCollection. (Default: True).

drop_index()

Drops an indexes present on this table collection. If the table are not currently indexed this method has no effect.

has_index()

Returns True if this TableCollection is indexed.

keep_intervals(intervals, simplify=True, record_provenance=True)

Delete all information from this set of tables which lies outside the specified list of genomic intervals. This is identical to TreeSequence.keep_intervals() but acts in place to alter the data in this TableCollection.

Parameters
• intervals (array_like) – A list (start, end) pairs describing the genomic intervals to keep. Intervals must be non-overlapping and in increasing order. The list of intervals must be interpretable as a 2D numpy array with shape (N, 2), where N is the number of intervals.

• simplify (bool) – If True, run simplify on the tables so that nodes no longer used are discarded. (Default: True).

• record_provenance (bool) – If True, add details of this operation to the provenance table in this TableCollection. (Default: True).

map_ancestors(samples, ancestors)

Returns an EdgeTable instance describing a subset of the genealogical relationships between the nodes insamples and ancestors.

Each row parent, child, left, right in the output table indicates that child has inherited the segment [left, right) from parent more recently than from any other node in these lists.

In particular, suppose samples is a list of nodes such that time is 0 for each node, and ancestors is a list of nodes such that time is greater than 0.0 for each node. Then each row of the output table will show an interval [left, right) over which a node in samples has inherited most recently from a node in ancestors, or an interval over which one of these ancestors has inherited most recently from another node in ancestors.

The following table shows which parent->child pairs will be shown in the output of map_ancestors. A node is a relevant descendant on a given interval if it also appears somewhere in the parent column of the outputted table.

 Type of relationship Shown in output of map_ancestors ancestor->sample Always ancestor1->ancestor2 Only if ancestor2 has a relevant descendant sample1->sample2 Always sample->ancestor Only if ancestor has a relevant descendant

The difference between samples and ancestors is that information about the ancestors of a node in ancestors will only be retained if it also has a relevant descendant, while information about the ancestors of a node in samples will always be retained. The node IDs in parent and child refer to the IDs in the node table of the inputted tree sequence.

The supplied nodes must be non-empty lists of the node IDs in the tree sequence: in particular, they do not have to be samples of the tree sequence. The lists of samples and ancestors may overlap, although adding a node from samples to ancestors will not change the output. So, setting samples and ancestors to the same list of nodes will find all genealogical relationships within this list.

If none of the nodes in ancestors or samples are ancestral to samples anywhere in the tree sequence, an empty table will be returned.

Parameters
• samples (list[int]) – A list of node IDs to retain as samples.

• ancestors (list[int]) – A list of node IDs to use as ancestors.

Returns

An EdgeTable instance displaying relationships between the samples and ancestors.

simplify(samples=None, filter_zero_mutation_sites=None, reduce_to_site_topology=False, filter_populations=True, filter_individuals=True, filter_sites=True, keep_unary=False)

Simplifies the tables in place to retain only the information necessary to reconstruct the tree sequence describing the given samples. This will change the ID of the nodes, so that the node samples[k] will have ID k in the result. The resulting NodeTable will have only the first len(samples) individuals marked as samples. The mapping from node IDs in the current set of tables to their equivalent values in the simplified tables is also returned as a numpy array. If an array a is returned by this function and u is the ID of a node in the input table, then a[u] is the ID of this node in the output table. For any node u that is not mapped into the output tables, this mapping will equal -1.

Tables operated on by this function must: be sorted (see TableCollection.sort()), have children be born strictly after their parents, and the intervals on which any individual is a child must be disjoint. Other than this the tables need not satisfy remaining requirements to specify a valid tree sequence (but the resulting tables will).

This is identical to TreeSequence.simplify() but acts in place to alter the data in this TableCollection. Please see the TreeSequence.simplify() method for a description of the remaining parameters.

Parameters
• samples (list[int]) – A list of node IDs to retain as samples. If not specified or None, use all nodes marked with the IS_SAMPLE flag.

• filter_zero_mutation_sites (bool) – Deprecated alias for filter_sites.

• reduce_to_site_topology (bool) – Whether to reduce the topology down to the trees that are present at sites. (default: False).

• filter_populations (bool) – If True, remove any populations that are not referenced by nodes after simplification; new population IDs are allocated sequentially from zero. If False, the population table will not be altered in any way. (Default: True)

• filter_individuals (bool) – If True, remove any individuals that are not referenced by nodes after simplification; new individual IDs are allocated sequentially from zero. If False, the individual table will not be altered in any way. (Default: True)

• filter_sites (bool) – If True, remove any sites that are not referenced by mutations after simplification; new site IDs are allocated sequentially from zero. If False, the site table will not be altered in any way. (Default: True)

• keep_unary (bool) – If True, any unary nodes (i.e. nodes with exactly one child) that exist on the path from samples to root will be preserved in the output. (Default: False)

Returns

A numpy array mapping node IDs in the input tables to their corresponding node IDs in the output tables.

Return type

numpy array (dtype=np.int32)

sort(edge_start=0)

Sorts the tables in place. This ensures that all tree sequence ordering requirements listed in the Valid tree sequence requirements section are met, as long as each site has at most one mutation (see below).

If the edge_start parameter is provided, this specifies the index in the edge table where sorting should start. Only rows with index greater than or equal to edge_start are sorted; rows before this index are not affected. This parameter is provided to allow for efficient sorting when the user knows that the edges up to a given index are already sorted.

The individual, node, population and provenance tables are not affected by this method.

Edges are sorted as follows:

• time of parent, then

• parent node ID, then

• child node ID, then

• left endpoint.

Note that this sorting order exceeds the edge sorting requirements for a valid tree sequence. For a valid tree sequence, we require that all edges for a given parent ID are adjacent, but we do not require that they be listed in sorted order.

Sites are sorted by position, and sites with the same position retain their relative ordering.

Mutations are sorted by site ID, and mutations with the same site retain their relative ordering. This does not currently rearrange tables so that mutations occur after their mutation parents, which is a requirement for valid tree sequences.

Parameters

edge_start (int) – The index in the edge table where sorting starts (default=0; must be <= len(edges)).

tree_sequence()

Returns a TreeSequence instance with the structure defined by the tables in this TableCollection. If the table collection is not in canonical form (i.e., does not meet sorting requirements) or cannot be interpreted as a tree sequence an exception is raised. The sort() method may be used to ensure that input sorting requirements are met.

Returns

A TreeSequence instance reflecting the structures defined in this set of tables.

Return type

TreeSequence

Table functions¶

tskit.parse_nodes(source, strict=True, encoding='utf8', base64_metadata=True, table=None)

Parse the specified file-like object containing a whitespace delimited description of a node table and returns the corresponding NodeTable instance. See the node text format section for the details of the required format and the node table definition section for the required properties of the contents.

See load_text() for a detailed explanation of the strict parameter.

Parameters
• source (stream) – The file-like object containing the text.

• strict (bool) – If True, require strict tab delimiting (default). If False, a relaxed whitespace splitting algorithm is used.

• encoding (string) – Encoding used for text representation.

• base64_metadata (bool) – If True, metadata is encoded using Base64 encoding; otherwise, as plain text.

• table (NodeTable) – If specified write into this table. If not, create a new NodeTable instance.

tskit.parse_edges(source, strict=True, table=None)

Parse the specified file-like object containing a whitespace delimited description of a edge table and returns the corresponding EdgeTable instance. See the edge text format section for the details of the required format and the edge table definition section for the required properties of the contents.

See load_text() for a detailed explanation of the strict parameter.

Parameters
• source (stream) – The file-like object containing the text.

• strict (bool) – If True, require strict tab delimiting (default). If False, a relaxed whitespace splitting algorithm is used.

• table (EdgeTable) – If specified, write the edges into this table. If not, create a new EdgeTable instance and return.

tskit.parse_sites(source, strict=True, encoding='utf8', base64_metadata=True, table=None)

Parse the specified file-like object containing a whitespace delimited description of a site table and returns the corresponding SiteTable instance. See the site text format section for the details of the required format and the site table definition section for the required properties of the contents.

See load_text() for a detailed explanation of the strict parameter.

Parameters
• source (stream) – The file-like object containing the text.

• strict (bool) – If True, require strict tab delimiting (default). If False, a relaxed whitespace splitting algorithm is used.

• encoding (string) – Encoding used for text representation.

• base64_metadata (bool) – If True, metadata is encoded using Base64 encoding; otherwise, as plain text.

• table (SiteTable) – If specified write site into this table. If not, create a new SiteTable instance.

tskit.parse_mutations(source, strict=True, encoding='utf8', base64_metadata=True, table=None)

Parse the specified file-like object containing a whitespace delimited description of a mutation table and returns the corresponding MutationTable instance. See the mutation text format section for the details of the required format and the mutation table definition section for the required properties of the contents.

See load_text() for a detailed explanation of the strict parameter.

Parameters
• source (stream) – The file-like object containing the text.

• strict (bool) – If True, require strict tab delimiting (default). If False, a relaxed whitespace splitting algorithm is used.

• encoding (string) – Encoding used for text representation.

• base64_metadata (bool) – If True, metadata is encoded using Base64 encoding; otherwise, as plain text.

• table (MutationTable) – If specified, write mutations into this table. If not, create a new MutationTable instance.

tskit.pack_strings(strings, encoding='utf8')

Packs the specified list of strings into a flattened numpy array of 8 bit integers and corresponding offsets using the specified text encoding. See Encoding ragged columns for details of this encoding of columns of variable length data.

Parameters
• data (list[str]) – The list of strings to encode.

• encoding (str) – The text encoding to use when converting string data to bytes. See the codecs module for information on available string encodings.

Returns

The tuple (packed, offset) of numpy arrays representing the flattened input data and offsets.

Return type

numpy.array (dtype=np.int8), numpy.array (dtype=np.uint32)

tskit.unpack_strings(packed, offset, encoding='utf8')

Unpacks a list of strings from the specified numpy arrays of packed byte data and corresponding offsets using the specified text encoding. See Encoding ragged columns for details of this encoding of columns of variable length data.

Parameters
• packed (numpy.ndarray) – The flattened array of byte values.

• offset (numpy.ndarray) – The array of offsets into the packed array.

• encoding (str) – The text encoding to use when converting string data to bytes. See the codecs module for information on available string encodings.

Returns

The list of strings unpacked from the parameter arrays.

Return type

list[str]

tskit.pack_bytes(data)

Packs the specified list of bytes into a flattened numpy array of 8 bit integers and corresponding offsets. See Encoding ragged columns for details of this encoding.

Parameters

data (list[bytes]) – The list of bytes values to encode.

Returns

The tuple (packed, offset) of numpy arrays representing the flattened input data and offsets.

Return type

numpy.array (dtype=np.int8), numpy.array (dtype=np.uint32)

tskit.unpack_bytes(packed, offset)

Unpacks a list of bytes from the specified numpy arrays of packed byte data and corresponding offsets. See Encoding ragged columns for details of this encoding.

Parameters
• packed (numpy.ndarray) – The flattened array of byte values.

• offset (numpy.ndarray) – The array of offsets into the packed array.

Returns

The list of bytes values unpacked from the parameter arrays.

Return type

Note

This API will soon be deprecated in favour of multi-site extensions to the Statistics API.

class tskit.LdCalculator(tree_sequence)

Class for calculating linkage disequilibrium coefficients between pairs of mutations in a TreeSequence. This class requires the numpy library.

This class supports multithreaded access using the Python threading module. Separate instances of LdCalculator referencing the same tree sequence can operate in parallel in multiple threads.

Note

This class does not currently support sites that have more than one mutation. Using it on such a tree sequence will raise a LibraryError with an “Unsupported operation” message.

Parameters

tree_sequence (TreeSequence) – The tree sequence containing the mutations we are interested in.

r2(a, b)

Returns the value of the $$r^2$$ statistic between the pair of mutations at the specified indexes. This method is not an efficient method for computing large numbers of pairwise; please use either r2_array() or r2_matrix() for this purpose.

Parameters
• a (int) – The index of the first mutation.

• b (int) – The index of the second mutation.

Returns

The value of $$r^2$$ between the mutations at indexes a and b.

Return type

float

r2_array(a, direction=1, max_mutations=None, max_distance=None)

Returns the value of the $$r^2$$ statistic between the focal mutation at index $$a$$ and a set of other mutations. The method operates by starting at the focal mutation and iterating over adjacent mutations (in either the forward or backwards direction) until either a maximum number of other mutations have been considered (using the max_mutations parameter), a maximum distance in sequence coordinates has been reached (using the max_distance parameter) or the start/end of the sequence has been reached. For every mutation $$b$$ considered, we then insert the value of $$r^2$$ between $$a$$ and $$b$$ at the corresponding index in an array, and return the entire array. If the returned array is $$x$$ and direction is tskit.FORWARD then $$x[0]$$ is the value of the statistic for $$a$$ and $$a + 1$$, $$x[1]$$ the value for $$a$$ and $$a + 2$$, etc. Similarly, if direction is tskit.REVERSE then $$x[0]$$ is the value of the statistic for $$a$$ and $$a - 1$$, $$x[1]$$ the value for $$a$$ and $$a - 2$$, etc.

Parameters
• a (int) – The index of the focal mutation.

• direction (int) – The direction in which to travel when examining other mutations. Must be either tskit.FORWARD or tskit.REVERSE. Defaults to tskit.FORWARD.

• max_mutations (int) – The maximum number of mutations to return $$r^2$$ values for. Defaults to as many mutations as possible.

• max_distance (float) – The maximum absolute distance between the focal mutation and those for which $$r^2$$ values are returned.

Returns

An array of double precision floating point values representing the $$r^2$$ values for mutations in the specified direction.

Return type

numpy.ndarray

Warning

For efficiency reasons, the underlying memory used to store the returned array is shared between calls. Therefore, if you wish to store the results of a single call to get_r2_array() for later processing you must take a copy of the array!

r2_matrix()

Returns the complete $$m \times m$$ matrix of pairwise $$r^2$$ values in a tree sequence with $$m$$ mutations.

Returns

An 2 dimensional square array of double precision floating point values representing the $$r^2$$ values for all pairs of mutations.

Return type

numpy.ndarray

Provenance¶

We provide some preliminary support for validating JSON documents against the provenance schema. Programmatic access to provenance information is planned for future versions.

tskit.validate_provenance(provenance)

Validates the specified dict-like object against the tskit provenance schema. If the input does not represent a valid instance of the schema an exception is raised.

Parameters

provenance (dict) – The dictionary representing a JSON document to be validated against the schema.

Raises

ProvenanceValidationError

tskit.ProvenanceValidationError