phylo2owl.py

#!/usr/bin/env python

"""
phylo2owl.py: Convert phylogenies into OWL ontologies.
"""

import os.path
import sys
import argparse
import dendropy
import pystache

__version__ = "0.1"
__author__ = "Gaurav Vaidya"
__copyright__ = "Copyright 2016 The Phyloreferencing Project"

# List of supported formats
# Based on formats supported by DendroPy,
# see https://pythonhosted.org/DendroPy/schemas/index.html#specifying-the-data-source-format
INPUT_FORMATS = ["newick", "nexus", "nexml"]
DEFAULT_FORMAT = "newick"

# Main function
def main():
    """ Main function for the phylo2owl.py script """

    output_name = 'example'
    input_file = sys.stdin
    output_file = sys.stdout

    # Step 1. Parse command line arguments
    cmdline_parser = argparse.ArgumentParser(
        description="Convert phylogenies into OWL ontologies."
    )
    cmdline_parser.add_argument(
        'input_filename',
        metavar='input.tre',
        type=str,
        nargs='?',
        help='Phylogeny file to parse'
    )
    cmdline_parser.add_argument(
        '-f', '--format',
        dest='input_format',
        nargs='?',
        type=str.lower, # Lowercase input type name.
        choices=INPUT_FORMATS,
        default=DEFAULT_FORMAT,
        help='Input format (for input filename or standard input)'
    )
    cmdline_parser.add_argument(
        '-o',
        dest='output_filename',
        metavar='output.owl',
        type=str,
        help='Ontology file to output'
    )
    cmdline_parser.add_argument(
        '-n', '--name',
        dest='output_name',
        metavar='output_name',
        type=str,
        help='Name of the resource to emit'
    )
    cmdline_parser.add_argument(
        '-v', '--version',
        action='version',
        version='%(prog)s ' + __version__
    )
    cmdline_parser.add_argument(
        '--verbose',
        dest='flag_verbose',
        default=False,
        action='store_true',
        help='Display debugging information'
    )
    args = cmdline_parser.parse_args()

    # Set up FLAG_VERBOSE.
    flag_verbose = args.flag_verbose

    # Step 2. Set up input and output streams.
    # Try opening the input file.
    if args.input_filename:
        input_file = open(args.input_filename, 'r')

    # Figure out where the output should go, as well as the output name.
    if args.output_filename:
        output_file = open(args.output_filename, 'w')
        output_name = os.path.splitext(os.path.basename(args.output_filename))[0]
    elif args.input_filename:
        output_name = os.path.splitext(os.path.basename(args.input_filename))[0]

    # But override output name if explicitly provided.
    if args.output_name:
        output_name = args.output_name

    # TODO: Make sure output_name is a valid entity name, probably as defined
    # here -- https://www.w3.org/TR/REC-xml/#NT-NameChar

    if flag_verbose:
        sys.stderr.write("Output name: {0}\n".format(output_name))
        sys.stderr.write("Input file: {0}\n".format(input_file))
        sys.stderr.write("Output file: {0}\n".format(output_file))

    # Step 2. Use DendroPy to read input tree.
    try:
        tree = dendropy.Tree.get(file=input_file, schema=args.input_format)
    except dendropy.utility.error.DataParseError as err:
        sys.stderr.write("Error: could not parse input!\n{0}\n".format(err))
        sys.exit(1)

    if flag_verbose:
        sys.stderr.write("Tree read successfully: {0}\n".format(tree))

    # Step 3. Set up pystache to read templates.
    render = pystache.Renderer(missing_tags='strict')

    # Step 4. Write out the header.
    xmlbase = "http://phyloinformatics.net/phylo/{0}".format(output_name)
    xmlns = xmlbase + '#'
    output_file.write(render.render_path('templates/header.txt', {
        'name': output_name,
        'xmlbase': xmlbase,
        'xmlns': xmlbase + '#'
    }))

    # Step 5. Make a list of names for every node on this tree.
    node_names = dict()
    node_count = 1
    for node in tree:
        name = node.label

        if node.taxon:
            name = node.taxon.label.replace(' ', '_')

        if name is None:
            name = 'Node_{0}'.format(node_count)
            node_count += 1

        node_names[node] = name

    if flag_verbose:
        sys.stderr.write("Names assigned to {0} tree nodes:\n".format(len(node_names)))
        for (node, name) in node_names.items():
            sys.stderr.write(" - {0}: {1}\n".format(name, node))
        sys.stderr.write("\n")

    # Step 6. Write out each node on the tree.
    node_count = 1
    for node in tree:
        output_file.write(render.render_path('templates/individual.txt', {
            'xmlns': xmlns,
            'term': node_names[node],
            'name': output_name,
            'children': [{'child': node_names[n]} for n in node.child_nodes()],
            'siblings': [{'sibling': node_names[n]} for n in node.sibling_nodes()]
        }))

    # Step 7. Write out the footer.
    output_file.write(render.render_path('templates/footer.txt'))
    sys.exit(0)

if __name__ == '__main__':
    main()