pylogeny.newick module

Newick string parsing and object interaction. A Newick string can represent a phylogenetic tree.

exception pylogeny.newick.ParsingError(val)

Bases: exceptions.Exception

__init__(val)

pylogeny.newick.assignParents(top)

Should be a one-time use function. Goes through and assigns parents to the parsed newick tree structure nodes and branches to allow for up-traversal.

Parameters:top (a node object) – a top-level node for a tree (root node)

class pylogeny.newick.branch(chi, l, parent=None, s=None)

Bases: pylogeny.base.treeBranch

Branch for a tree parsed from a Newick string.

__init__(chi, l, parent=None, s=None)

Initialize a branch in a tree parsed from a Newick string.

Parameters:

• chi (a node object) – a child node
• l (a floating point value) – a branch length
• parent (a node object) – an optional parent node; default none

pylogeny.newick.getAllBranches(br)

Given a branch, traverse subtree and return comprising branches as a list.

Parameters:br (a branch object) – a branch from a tree

pylogeny.newick.getBalancingBracket(newick, i)

Given a position of an opening bracket in a newick string, i, output the closing bracket’s position that corresponds to this opening bracket.

Parameters:

• newick (a string) – a Newick string
• i (an integer < length of the string) – a position in the string (index)

Returns:

an integer

pylogeny.newick.getBranchLength(newick, i)

Given a position of a colon symbol (indicating a branch length), return the branch length.

Parameters:

• newick (a string) – a Newick string
• i (an integer < length of the string) – a position in the string (index)

Returns:

an integer

pylogeny.newick.getLeafName(newick, i)

Given the position of a leaf, find its complete name.

Parameters:

• newick (a string) – a Newick string
• i (an integer < length of the string) – a position in the string (index)

Returns:

an integer

pylogeny.newick.invertAlongPathToNode(target, top)

DANGEROUS: Reverses all directionality to a given node from a top-level node. Intended as a low-level function for rerooting a tree.

Parameters:

• target (a node object) – a target node
• top (a node object) – a top-level node for a tree (root node)

pylogeny.newick.isSibling(br, other)

Given a branch, determine if that branch is adjacent to another branch.

Parameters:

• br (a branch object) – a branch from a tree
• other (a branch object) – another branch from a tree

class pylogeny.newick.newickParser(newick)

Parsing object for Newick strings.

__init__(newick)

Initialize this parser (with a Newick string).

Parameters:newick (a string) – a Newick string

parse()

Parse the stored newick string into a topological structure.

Returns:the top-level root node object

class pylogeny.newick.node(lbl='', children=None, parent=None)

Bases: pylogeny.base.treeNode

Node for a tree parsed from a Newick string.

__init__(lbl='', children=None, parent=None)

Initialize a node in a tree parsed from a Newick string.

Parameters:

• lbl (a string) – a label for this node
• children (a list of branch objects) – an optional set of children (branches); default none
• parent (a branch object) – an optional parent branch for this node; default none

pylogeny.newick.parseNewick(newick, i, j, top)

Parse a newick string into a topological newick structure given a top-level node.

Parameters:

• newick (a string) – a Newick string
• i (an integer) – a starting position to start parsing
• j (an integer) – an end position to stop parsing
• top (a node object) – a top-level node; start parsing with None

pylogeny.newick.removeBranchLengths(top)

Goes through and removes any stored branch lengths.

Parameters:top (a node object) – a top-level node for a tree (root node)

pylogeny.newick.removeUnaryInternalNodes(top)

Goes through and ensures any degree-2 internal nodes are smoothed into a single degree-3 internal node.

Parameters:top (a node object) – a top-level node for a tree (root node)

pylogeny.newick.shuffleLeaves(top)

DANGEROUS: Given a top-level node, shuffle all leaves in this tree.

Parameters:top (a node object) – a top-level node for a tree (root node)