splitp.parsers package
Submodules
splitp.parsers.fasta module
- splitp.parsers.fasta.fasta_to_dict(path_to_file)
- splitp.parsers.fasta.get_pattern_counts(alignment)
- splitp.parsers.fasta.pattern_counts_to_probs(patterns, seqLen)
- splitp.parsers.fasta.pattern_probs_from_alignment(path_to_file, return_sequence_length=False)
- splitp.parsers.fasta.read_alignment_from_file(path_to_file)
splitp.parsers.newick module
- splitp.parsers.newick.json_to_newick(json_dict, namestring='id', lengthstring='branch_length', childrenstring='children')
Converts a JSON tree to a newick string
- Arguments:
json_dict: The JSON tree to convert to newick.
- splitp.parsers.newick.move_tree_edge_labels_to_nodes(tree, remove_edge_attributes=True)
Every node is given all of the attributes of it’s in-edge
- Arguments:
tree: The tree to move edge labels to nodes in. remove_edge_attributes: Whether or not to remove the edge attributes after moving them to the nodes.
- splitp.parsers.newick.newick_to_json(newick_string, namestring='id', lengthstring='branch_length', childrenstring='children', generate_names=False)
Parses a newick string (example “((A,B),C)”) into JSON format accepted by NetworkX
- Arguments:
- newick_string: The newick string to convert to JSON. Names, branch lengths and named
internal nodes accepted. If no names are given, an ID is generated for the name if generate_names=True.
namestring: The label for node name to use in the JSON (default “id”). lengthstring: The label for branch length to use in the JSON (default “branch_length”). childrenstring: The label for children arrays to use in the JSON (default “children”). generate_names: Whether or not to generate names if none are given
- splitp.parsers.newick.strip_newick(newick)