@@ -7,20 +7,43 @@ """ __docformat__ = "epytext en" +from itertools import chain + from Bio.Nexus import Nexus +# Structure of a Nexus tree-only file +NEX_TEMPLATE = """\ +#NEXUS +Begin Taxa; + Dimensions NTax=%(count)d; + TaxLabels %(labels)s; +End; +Begin Trees; + %(trees)s +End; +""" + +# 'index' starts from 1; 'tree' is the Newick tree string +TREE_TEMPLATE = "Tree tree%(index)d=[&U]%(tree)s;" + def parse(file): nex = Nexus.Nexus(file) return iter(nex.trees) +# XXX Nexus/Newick-specific tree attributes: to_string, get_taxa def write(obj, file, **kwargs): - raise NotImplementedError("This function doesn't work yet.") - nex = Nexus.Nexus() - if isinstance(obj, list): - nex.trees = obj - else: - nex.trees = list(obj) - Nexus.Nexus.write_nexus_data(nex, file, **kwargs) - return len(nex.trees) + trees = list(obj) + nexus_trees = [TREE_TEMPLATE % { + 'index': idx+1, + 'tree': tree.to_string(plain_newick=True, plain=False, **kwargs) + } for idx, tree in enumerate(trees)] + tax_labels = list(chain(*(t.get_taxa() for t in trees))) + text = NEX_TEMPLATE % { + 'count': len(tax_labels), + 'labels': ' '.join(tax_labels), + 'trees': '\n'.join(nexus_trees), + } + file.write(text) + return len(nexus_trees) Bio/TreeIO/NexusIO.py @@ -73,7 +73,7 @@ def write(trees, file, format, **kwargs): trees = [trees] do_close = False if isinstance(file, basestring): - file = open(file, 'r') + file = open(file, 'w+') do_close = True try: n = getattr(supported_formats[format], 'write')(trees, file, **kwargs) Bio/TreeIO/__init__.py ac2facc6c70b521a9655d996bfd741ef45f6945a Eric Talevich eric.talevich@gmail.com http://github.com/etal/biopython/commit/e0c560f017f9971e8e57fd5e76bbabfbef1a5baf e0c560f017f9971e8e57fd5e76bbabfbef1a5baf 2009-10-13T12:54:24-07:00 2009-10-13T12:54:24-07:00 TreeIO: Fixed NexusIO.write support. It doesn't actually use any Nexus methods, just fills in a template based on the output of Forester with an example file. 2fda30e0d87328158a7b634dedfe7d2afcc84bed Eric Talevich eric.talevich@gmail.com