コード例 #1
0
ファイル: tree.py プロジェクト: ChriZiegler/ivy
def readmany(data, format="newick"):
    """Iterate over trees from a source."""
    if type(data) in types.StringTypes:
        if os.path.isfile(data):
            data = open(data)
        else:
            data = StringIO(data)

    if format == "newick":
        for line in data:
            yield newick.parse(line)
    elif format == "nexus":
        for rec in newick.nexus_iter(data):
            yield rec.parse()
    else:
        raise Exception, "format '%s' not recognized" % format
    data.close()
コード例 #2
0
ファイル: tree.py プロジェクト: ChriZiegler/ivy
def read(data, format=None, treename=None, ttable=None):
    """
    Read a single tree from *data*, which can be a Newick string, a
    file name, or a file-like object with `tell` and 'read`
    methods. *treename* is an optional string that will be attached to
    all created nodes.

    Args:
        data: A file or file-like object or newick string

    Returns:
        Node: The root node.
    """
    import newick
    StringTypes = types.StringTypes

    def strip(s):
        fname = os.path.split(s)[-1]
        head, tail = os.path.splitext(fname)
        tail = tail.lower()
        if tail in (".nwk", ".tre", ".tree", ".newick", ".nex"):
            return head
        else:
            return fname

    if (not format):
        if (type(data) in StringTypes) and os.path.isfile(data):
            s = data.lower()
            for tail in ".nex", ".nexus", ".tre":
                if s.endswith(tail):
                    format="nexus"
                    break

    if (not format):
        format = "newick"

    if format == "newick":
        if type(data) in StringTypes:
            if os.path.isfile(data):
                treename = strip(data)
                return newick.parse(file(data), treename=treename,
                                    ttable=ttable)
            else:
                return newick.parse(data, ttable=ttable)

        elif (hasattr(data, "tell") and hasattr(data, "read")):
            treename = strip(getattr(data, "name", None))
            return newick.parse(data, treename=treename, ttable=ttable)
    elif format == "nexus-dendropy":
        import dendropy
        if type(data) in StringTypes:
            if os.path.isfile(data):
                treename = strip(data)
                return newick.parse(
                    str(dendropy.Tree.get_from_path(data, "nexus")),
                    treename=treename
                    )
            else:
                return newick.parse(
                    str(dendropy.Tree.get_from_string(data, "nexus"))
                    )

        elif (hasattr(data, "tell") and hasattr(data, "read")):
            treename = strip(getattr(data, "name", None))
            return newick.parse(
                str(dendropy.Tree.get_from_stream(data, "nexus")),
                treename=treename
                )
        else:
            pass

    elif format == "nexus":
        if type(data) in StringTypes:
            if os.path.isfile(data):
                with open(data) as infile:
                    rec = newick.nexus_iter(infile).next()
                    if rec: return rec.parse()
            else:
                rec = newick.nexus_iter(StringIO(data)).next()
                if rec: return rec.parse()
        else:
            rec = newick.nexus_iter(data).next()
            if rec: return rec.parse()
    else:
        # implement other tree formats here (nexus, nexml etc.)
        raise IOError, "format '%s' not implemented yet" % format

    raise IOError, "unable to read tree from '%s'" % data