treemaker package

Submodules

treemaker.test_treemaker module

class treemaker.test_treemaker.Test_ParseArgs(methodName='runTest')

Bases: unittest.case.TestCase

test_IOError_on_no_file()

test_parse_filename_and_full_output()

test_parse_filename_and_output()

test_parse_filename_only()

test_parse_mode()

test_parse_nodelabels()

class treemaker.test_treemaker.Test_Tree(methodName='runTest')

Bases: unittest.case.TestCase

test_add()

test_conflicts()

test_deep_tree()

test_empty_tree()

test_eq()

test_example()

test_get()

test_get_or_create()

test_gt()

test_is_node()

test_is_tip()

test_lt()

test_real()

test_recursive_add()

test_repr()

test_sanitise()

test_simple()

test_singleton_tree()

test_tips()

class treemaker.test_treemaker.Test_TreeMaker(methodName='runTest')

Bases: unittest.case.TestCase

test_add()

test_add_2()

test_add_from()

test_add_from_exception()

test_error_on_bad_taxon()

test_error_on_duplicate()

test_parse_classification()

class treemaker.test_treemaker.Test_TreeMakerIO(methodName='runTest')

Bases: unittest.case.TestCase

Test the IO functionality of TreeMaker in its own test class as we need some setup/teardown logic.

classmethod setUpClass()

Hook method for setting up class fixture before running tests in the class.

classmethod tearDownClass()

Hook method for deconstructing the class fixture after running all tests in the class.

test_read()

test_read_error_on_malformed()

test_read_skips_empty_lines()

test_read_with_tabs()

test_write_newick()

test_write_nexus()

test_write_nexus_error_on_bad_method()

test_write_to_file_error_on_existing_file()

test_write_to_file_error_on_invalid_mode()

test_write_to_newick()

test_write_to_nexus()

class treemaker.test_treemaker.Test_Tree_Nodelabels(methodName='runTest')

Bases: unittest.case.TestCase

test_deep_tree()

test_example()

test_real()

test_recursive_add()

test_simple()

treemaker.treemaker module

TreeMaker

class treemaker.treemaker.Tree(node=None, children=None, show_nodelabels=False)

Bases: object

Tree object to represent the classification taxonomy.

Parameters:

• node (str) – Label for this node.
• children (list) – Optional list of children nodes
• show_nodelabels (boolean) – A flag to show nodelabels or not (default=False)

add(node, children=None)

Adds a node (with optional children) to the tree.

Parameters:

• node (str) – Label for this node.
• children (list) – Optional list of children nodes

Returns:

the created node matching label.

Return type:

treemaker.Tree

get(label, node=None)

Searches tree for node label.

Parameters:

• label (str) – Label for this node.
• node (treemaker.Tree) – (optional) parent node. Default is current node.

Returns:

the found or created node matching label.

Return type:

treemaker.Tree

get_or_create(label)

Helper function to get or create a node.

Parameters:label (str) – Label for this node. Returns:the found or created node matching label. Return type:treemaker.Tree

is_node

Returns True if node is a node (i.e. has children)

is_tip

Returns True if node is a tip

tips(node=None)

Returns a list of the tips in the tree

Parameters:node (treemaker.Tree) – (optional) parent node. Default is current node. Returns:the tip nodes from the given node. Return type:List[treemaker.Tree]

class treemaker.treemaker.TreeMaker(label='root', nodelabels=False)

Bases: object

add(leaf, classification)

Adds leaf to the tree in the location specified by classification

Parameters:

• leaf (str) – Leaf label
• classification (str) – A classification string of a format handled by parse_classification.

Returns:

the tree with the new node added.

Return type:

treemaker.Tree

Raises:

ValueError – If a duplicate leaf label or classification is given.

add_from(iterable)

Adds all entries from an iterable. iterable should be a list of lists or a list of tuples (etc) with 2 values - the first one the taxon name, the second the classification string, e.g.

>>> iterable = [
>>>     ['taxon1', 'a, a'],
>>>     ['taxon2', 'a, b'],
>>> ]
>>> tree = TreeMaker().add_from(iterable)

Parameters:iterable (iter) – an iterable (e.g. a list). Returns:the tree with the new nodes added. Return type:treemaker.Tree Raises:ValueError – If each member of the iterable does not contain two entries (leaf name, and classification).

parse_classification(classification)

Parses a classification string into nodes.

>>> Tree().parse_classification("Indo-European, Germanic, English")
>>> ["Indo-European", "Germanic", "English"]

Parameters:classification (str) – a classification string e.g. “clade 1, clade 2, clade 3” Returns:a list of the classification nodes. Return type:List

read(filename)

Reads data from filename and constructs a tree.

filename should be formatted as follows:

Taxon1   FamilyA, GroupA, SubgroupA
Taxon2   FamilyA, GroupA, SubgroupB
Taxon3   FamilyA, GroupB
... etc

Parameters:filename (str) – a filename containing the classification. Returns:a Tree with the specified classification. Return type:treemaker.Tree Raises:ValueError – if a line in the file is not able to be parsed.

write(mode='newick')

Writes the output form of the tree.

Parameters:

• mode (str) – An output mode. One of: * “nexus” = a nexus file is generated * “newick” = a newick file (bare tree) is generated
• nodelabels (bool) – show nodelabels or not (default False)

Returns:

a string containing the formatted content.

Return type:

str

Raises:

ValueError – if mode is not “nexus” or “newick”.

write_to_file(filename, mode='nexus')

Writes the tree to filename.

Parameters:

• mode (str) – An output mode. One of: * “nexus” = a nexus file is generated * “newick” = a newick file (bare tree) is generated
• nodelabels (bool) – show nodelabels or not (default False)

Returns:

None

Raises:

• IOError – if filename already exists.
• ValueError – if mode is not “nexus” or “newick”.

treemaker.treemaker.main(args=None)

treemaker.treemaker.parse_args(args)

Parses command line arguments

Returns a tuple of (inputfile, method, outputfile)

Module contents