Input/Output

Classes for reading and writing sequence alignments and phylogenetic trees.

Sequence Alignment

Alignment

class crabml.io.sequences.Alignment(names, sequences, n_species, n_sites, seqtype)[source]

Multiple sequence alignment.

Attributes

nameslist[str]: Sequence names/labels
sequencesndarray, shape (n_species, n_sites): Encoded sequences as integer arrays
n_speciesint: Number of sequences
n_sitesint: Number of sites (alignment length)
seqtypestr: Sequence type (‘codon’, ‘aa’, ‘dna’)

names: list[str]

sequences: ndarray

n_species: int

n_sites: int

seqtype: str

classmethod from_phylip(filepath, seqtype='codon')[source]

Parse PHYLIP format alignment file.

Custom parser for PAML-style PHYLIP format (sequential). The first line contains n_sequences and sequence_length. Each sequence starts with a name line, followed by sequence data.

Return type:: Alignment

Parameters

filepathPath or str: Path to PHYLIP format file
seqtypestr: Sequence type: ‘codon’, ‘aa’, or ‘dna’

Returns

Alignment: Parsed alignment

Examples

>>> aln = Alignment.from_phylip("lysozyme.txt", seqtype='codon')
>>> aln.n_species
7
>>> aln.n_sites
130

classmethod from_fasta(filepath, seqtype='codon')[source]

Parse FASTA format alignment file.

Return type:: Alignment

Parameters

filepathPath or str: Path to FASTA format file
seqtypestr: Sequence type: ‘codon’, ‘aa’, or ‘dna’

Returns

Alignment: Parsed alignment

Examples

>>> aln = Alignment.from_fasta("alignment.fasta", seqtype='codon')

to_phylip(filepath)[source]

Write alignment to PHYLIP format file.

Return type:: None

Parameters

filepathPath or str: Output file path

to_fasta(filepath)[source]

Write alignment to FASTA format file.

Return type:: None

Parameters

filepathPath or str: Output file path

__init__(names, sequences, n_species, n_sites, seqtype)

Phylogenetic Trees

Tree

class crabml.io.trees.Tree(root, n_nodes, n_leaves, leaf_names)[source]

Phylogenetic tree.

Attributes

rootTreeNode: Root node of the tree
n_nodesint: Total number of nodes
n_leavesint: Number of leaf nodes
leaf_nameslist[str]: Names of leaf nodes

root: TreeNode

n_nodes: int

n_leaves: int

leaf_names: list[str]

classmethod from_newick(newick_string)[source]

Parse Newick format tree string.

Return type:: Tree

Parameters

newick_stringstr: Newick format tree

Returns

Tree: Parsed tree

postorder()[source]

Return nodes in post-order traversal (leaves to root).

Return type:: list[TreeNode]

Returns

list[TreeNode]: Nodes in post-order

get_branches()[source]

Get all branches as (parent, child) pairs.

Return type:: list[tuple[TreeNode, TreeNode]]

Returns

list[tuple[TreeNode, TreeNode]]: List of (parent, child) tuples for each branch

get_branch_labels()[source]

Get integer branch labels for branch-site models.

Converts string labels like ‘#0’, ‘#1’ to integers. Branches without labels are assigned 0 (background).

Return type:: list[int]

Returns

list[int]: Branch labels as integers (0=background, 1=foreground, etc.)

validate_branch_site_labels()[source]

Validate branch labels for branch-site models.

Branch-site models (Model A, A1) require exactly 2 label types: - 0 (background) - 1 (foreground)

Return type:: None

Raises

ValueError: If labels are not valid for branch-site models

to_newick()[source]

Convert tree to Newick format string.

Return type:: str

Returns

str: Tree in Newick format

__init__(root, n_nodes, n_leaves, leaf_names)