New upstream version 4.3.0+dfsg

Release 4.3.0

-------------

-   [SumTrees]: Important bugfix in tracking splits on consensus tree from rooted trees: previously it was possible for a split on the consensus tree to be ignored, resulting in a null (0) edge length and no (0.0) support.

-   Added ``sumlabels.py`` application.

-   BD tree (``dendropy.model.birth_death_tree``) now allows for preservation of extinct tips.

-   Improved performance of character subset export

Release 4.2.0

-------------

Metadata-Version: 1.1

Name: DendroPy

Version: 4.2.0

Version: 4.3.0

Summary: A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.

Home-page: http://packages.python.org/DendroPy/

Author: Jeet Sukumaran and Mark T. Holder

        Current Release

        ===============

        The current release of DendroPy is version 4.2.0 (master-5051a46, 2016-12-28 13:25:19).

        The current release of DendroPy is version 4.3.0 (master-e251bcf, 2017-07-06 21:23:19).

Keywords: phylogenetics phylogeny phylogenies phylogeography evolution evolutionary biology systematics coalescent population genetics phyloinformatics bioinformatics

Classifier: Programming Language :: Python :: 3.2

Classifier: Programming Language :: Python :: 3.3

Classifier: Programming Language :: Python :: 3.4

Classifier: Programming Language :: Python :: 3.5

Classifier: Programming Language :: Python :: 3.6

Classifier: Programming Language :: Python

Classifier: Topic :: Scientific/Engineering :: Bio-Informatics

DendroPy.egg-info/requires.txt

DendroPy.egg-info/top_level.txt

DendroPy.egg-info/zip-safe

applications/sumlabels/sumlabels.py

applications/sumtrees/sumtrees.py

dendropy/__init__.py

dendropy/__main__.py

dendropy/interop/muscle.py

dendropy/interop/paup.py

dendropy/interop/raxml.py

dendropy/interop/rspr.py

dendropy/interop/rstats.py

dendropy/interop/seqgen.py

dendropy/legacy/__init__.py

Metadata-Version: 1.1

Name: DendroPy

Version: 4.2.0

Version: 4.3.0

Summary: A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.

Home-page: http://packages.python.org/DendroPy/

Author: Jeet Sukumaran and Mark T. Holder

        Current Release

        ===============

        The current release of DendroPy is version 4.2.0 (master-5051a46, 2016-12-28 13:25:19).

        The current release of DendroPy is version 4.3.0 (master-e251bcf, 2017-07-06 21:23:19).

Keywords: phylogenetics phylogeny phylogenies phylogeography evolution evolutionary biology systematics coalescent population genetics phyloinformatics bioinformatics

Classifier: Programming Language :: Python :: 3.2

Classifier: Programming Language :: Python :: 3.3

Classifier: Programming Language :: Python :: 3.4

Classifier: Programming Language :: Python :: 3.5

Classifier: Programming Language :: Python :: 3.6

Classifier: Programming Language :: Python

Classifier: Topic :: Scientific/Engineering :: Bio-Informatics

#! /usr/bin/env python

##############################################################################

##  DendroPy Phylogenetic Computing Library.

##

##  Copyright 2010 Jeet Sukumaran and Mark T. Holder.

##  All rights reserved.

##

##  See "LICENSE.txt" for terms and conditions of usage.

##

##  If you use this work or any portion thereof in published work,

##  please cite it as:

##

##     Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library

##     for phylogenetic computing. Bioinformatics 26: 1569-1571.

##

##############################################################################

"""

Marge labels of splits/branches from different input trees onto corresponding

splits/branches of a single tree.

"""

import os

import sys

import argparse

import datetime

import time

import socket

try:

    import getpass

except:

    pass

import platform

import dendropy

from dendropy.utility.messaging import ConsoleMessenger

from dendropy.utility.cli import confirm_overwrite, show_splash

_program_name = "SumLabels"

_program_subtitle = "Phylogenetic Tree Label Concatenation"

_program_date = "Jan 20 2017"

_program_version = "Version 2.0.0 (%s)" % _program_date

_program_author = "Jeet Sukumaran"

_program_contact = "jeetsukumaran@gmail.com"

_program_copyright = "Copyright (C) 2017 Jeet Sukumaran.\n" \

                 "License GPLv3+: GNU GPL version 3 or later.\n" \

                 "This is free software: you are free to change\nand redistribute it. " \

                 "There is NO WARRANTY,\nto the extent permitted by law."

def main_cli():

    description =  "%s %s %s" % (_program_name, _program_version, _program_subtitle)

    parser = argparse.ArgumentParser(version =_program_version, description=description)

    parser.add_argument(

            "sources",

            metavar="TREEFILE",

            nargs="+")

    parser.add_argument("-t","--target",

            dest="target_tree_filepath",

            default=None,

            help="path to file with tree (Newick or NEXUS format) "

            + "to which labels will be written")

    parser.add_argument("--preserve-target-labels",

            action="store_true",

            dest="preserve_target_labels",

            default=False,

            help="keep any existing labels on target tree (by default, these will be cleared before writing the new labels)")

    parser.add_argument("--rooted",

            action="store_true",

            dest="rooted_trees",

            default=None,

            help="treat trees as rooted")

    parser.add_argument("--unrooted",

            action="store_false",

            dest="rooted_trees",

            default=None,

            help="treat trees as unrooted")

    parser.add_argument("--ignore-missing-source",

            action="store_true",

            dest="ignore_missing_source",

            default=False,

            help="ignore missing source tree files (at least one must exist!)")

    parser.add_argument("-o","--output",

            dest="output_filepath",

            default=None,

            help="path to output file (if not given, will print to standard output)")

    parser.add_argument("-s","--separator",

            dest="separator",

            default="/",

            help="string to use to separate labels from different source trees (default='%(default)s')")

    parser.add_argument("--no-taxa-block",

            action="store_false",

            dest="include_taxa_block",

            default=True,

            help="do not include a taxa block in the output treefile (otherwise will create taxa block by default)")

    parser.add_argument("-c", "--additional-comments",

            action="store",

            dest="additional_comments",

            default=None,

            help="additional comments to be added to the summary file")

    parser.add_argument("--to-newick",

            action="store_true",

            dest="to_newick_format",

            default=False,

            help="save results in NEWICK (PHYLIP) format (default is to save in NEXUS format)")

    parser.add_argument("--to-phylip",

            action="store_true",

            dest="to_newick_format",

            default=False,

            help="same as --to-newick")

    parser.add_argument("-r", "--replace",

            action="store_true",

            dest="replace",

            default=False,

            help="replace/overwrite output file without asking if it already exists ")

    parser.add_argument("-q", "--quiet",

            action="store_true",

            dest="quiet",

            default=False,

            help="suppress ALL logging, progress and feedback messages")

    args = parser.parse_args()

    if args.quiet:

        messaging_level = ConsoleMessenger.ERROR_MESSAGING_LEVEL

    else:

        messaging_level = ConsoleMessenger.INFO_MESSAGING_LEVEL

    messenger = ConsoleMessenger(name="SumLabels", messaging_level=messaging_level)

    # splash

    if not args.quiet:

        show_splash(prog_name=_program_name,

                prog_subtitle=_program_subtitle,

                prog_version=_program_version,

                prog_author=_program_author,

                prog_copyright=_program_copyright,

                dest=sys.stderr,

                )

    ###################################################

    # Source file idiot checking

    source_filepaths = []

    if len(args.sources) > 0:

        for fpath in args.sources:

            fpath = os.path.expanduser(os.path.expandvars(fpath))

            if not os.path.exists(fpath):

                if args.ignore_missing_source:

                    messenger.send_warning("Source file not found: '%s'" % fpath)

                else:

                    messenger.error("Terminating due to missing source files. "

                           + "Use the '--ignore-missing-source' option to continue even "

                           + "if some files are missing.")

                    sys.exit(1)

            else:

                source_filepaths.append(fpath)

        if len(source_filepaths) == 0:

            messenger.error("No valid sources of input trees specified. "

                    + "Please provide the path to at least one (valid and existing) file "

                    + "containing trees")

            sys.exit(1)

    else:

        messenger.info("No sources of input trees specified. "

                + "Please provide the path to at least one (valid and existing) file "

                + "containing tree samples to summarize. See '--help' for other options.")

        sys.exit(1)

    ###################################################

    # Lots of other idiot-checking ...

    # target tree

    if args.target_tree_filepath is not None:

        target_tree_filepath = os.path.expanduser(os.path.expandvars(args.target_tree_filepath))

        if not os.path.exists(target_tree_filepath):

            messenger.error("Target tree file not found: '%s'" % target_tree_filepath)

            sys.exit(1)

    else:

        messenger.error("Target tree file not specified: use the '-t' or '--target' option to provide path to target tree")

        sys.exit(1)

    # output

    if args.output_filepath is None:

        output_dest = sys.stdout

    else:

        output_fpath = os.path.expanduser(os.path.expandvars(args.output_filepath))

        if confirm_overwrite(filepath=output_fpath, replace_without_asking=args.replace):

            output_dest = open(output_fpath, "w")

        else:

            sys.exit(1)

    # taxon set to handle target trees

    master_taxon_namespace = dendropy.TaxonNamespace()

    is_rooted = args.rooted_trees

    messenger.info("Reading target tree: '%s'" % target_tree_filepath)

    target_tree = None

    if is_rooted:

        rooting = "force-rooted"

    else:

        rooting = None

    for tree in dendropy.Tree.yield_from_files(

            [target_tree_filepath, "rU",],

            schema='nexus/newick',

            taxon_namespace=master_taxon_namespace,

            rooting=rooting):

        target_tree = tree

        break

    bipartition_labels = {}

    for src_fpath in source_filepaths:

        messenger.info("Reading source tree(s) from: '%s'" % src_fpath)

        for tree in dendropy.Tree.yield_from_files(

                [src_fpath,],

                schema='nexus/newick',

                taxon_namespace=master_taxon_namespace,

                rooting=rooting):

            tree.encode_bipartitions()

            for bipartition, edge in tree.bipartition_edge_map.items():

                label = edge.head_node.label

                if not label:

                    continue

                try:

                    bipartition_labels[bipartition].append(label)

                except KeyError:

                    bipartition_labels[bipartition] = [label]

    messenger.info("Mapping labels")

    target_tree.encode_bipartitions()

    for bipartition, edge in target_tree.bipartition_edge_map.items():

        label = []

        if args.preserve_target_labels and edge.head_node.label:

            label.append(edge.head_node.label)

        elif not args.preserve_target_labels:

            edge.head_node.label = None

        if bipartition in bipartition_labels:

            label.extend(bipartition_labels[bipartition])

        else:

            pass

            # messenger.send_warning("Split on target tree not found in source trees: ignoring")

        if label:

            edge.head_node.label = args.separator.join(label)

    output_dataset = dendropy.DataSet()

    tree_list = output_dataset.new_tree_list(taxon_namespace=master_taxon_namespace)

    tree_list.append(target_tree)

    if args.to_newick_format:

        output_dataset.write(

                file=output_dest,

                schema="newick",

                suppress_rooting=False,

                suppress_edge_lengths=False,

                unquoted_underscores=False,

                preserve_spaces=False,

                store_tree_weights=False,

                suppress_annotations=False,

                annotations_as_nhx=False,

                suppress_item_comments=False,

                suppress_leaf_taxon_labels=False,

                suppress_leaf_node_labels=True,

                suppress_internal_taxon_labels=False,

                suppress_internal_node_labels=False,

                node_label_element_separator=' ',

                )

    else:

        if args.include_taxa_block:

            simple = False

        else:

            simple = True

        comment = []

        try:

            username = getpass.getuser()

        except:

            username = "a user"

        comment.append("%s %s by %s." % (_program_name, _program_version, _program_author))

        comment.append("Using DendroPy Version %s by Jeet Sukumaran and Mark T. Holder."

            % dendropy.__version__)

        python_version = sys.version.replace("\n", "").replace("[", "(").replace("]",")")

        comment.append("Running under Python %s on %s." % (python_version, sys.platform))

        comment.append("Executed on %s by %s@%s." % (platform.node(),  username, socket.gethostname()))

        if args.additional_comments:

            comment.append("\n")

            comment.append(args.additional_comments)

        output_dataset.write(

                file=output_dest,

                schema="nexus",

                simple=simple,

                file_comments=comment,

                suppress_rooting=False,

                unquoted_underscores=False,

                preserve_spaces=False,

                store_tree_weights=False,

                suppress_annotations=False,

                annotations_as_nhx=False,

                suppress_item_comments=False,

                suppress_leaf_taxon_labels=False,

                suppress_leaf_node_labels=True,

                suppress_internal_taxon_labels=False,

                suppress_internal_node_labels=False,

                node_label_element_separator=' ',

                )

    if not args.output_filepath:

        pass

    else:

        messenger.info("Results written to: '%s'." % (output_fpath))

if __name__ == '__main__':

    main_cli()