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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" 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.
##
##############################################################################
"""
Wrappers for interacting with the Biopython library.
"""
import tempfile
import re
from dendropy.utility import messaging
_LOG = messaging.get_logger(__name__)
import dendropy
DENDROPY_BIOPYTHON_INTEROPERABILITY = False
try:
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna, generic_rna, generic_nucleotide, generic_protein
DENDROPY_BIOPYTHON_INTEROPERABILITY = True
except ImportError:
_LOG.warn("BioPython could not be imported: BioPython interoperability not available")
else:
def as_biopython_object(o):
"""
Returns ``o`` as an biopython object.
"""
if isinstance(o, dendropy.CharacterMatrix):
if isinstance(o, dendropy.DnaCharacterMatrix):
bpa = generic_dna
elif isinstance(o, dendropy.RnaCharacterMatrix):
bpa = generic_rna
elif isinstance(o, dendropy.ProteinCharacterMatrix):
bpa = generic_protein
else:
raise ValueError("Character data type not supported in Biopython: '%s'" % type(o))
else:
raise ValueError("Invalid object type for conversion to Biopython: '%s'" % type(o))
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