def combine_nexuses(nexuslist):
"""
Combines a list of NexusReader instances into a single nexus
:param nexuslist: A list of NexusReader instances
:type nexuslist: List
:return: A NexusWriter instance
:raises TypeError: if nexuslist is not a list of NexusReader instances
:raises IOError: if unable to read an file in nexuslist
:raises NexusFormatException: if a nexus file does not have a `data` block
"""
out = NexusWriter()
charpos = 0
for nex_id, nex in enumerate(nexuslist, 1):
check_for_valid_NexusReader(nex, required_blocks=['data'])
if hasattr(nex, 'short_filename'):
nexus_label = os.path.splitext(nex.short_filename)[0]
else:
nexus_label = str(nex_id)
out.add_comment("%d - %d: %s" %
(charpos, charpos + nex.data.nchar - 1, nexus_label))
for site_idx, site in enumerate(sorted(nex.data.characters), 0):
data = nex.data.characters.get(site)
charpos += 1
# work out character label
charlabel = nex.data.charlabels.get(site_idx, site_idx + 1)
label = '%s.%s' % (nexus_label, charlabel)
for taxon, value in data.items():
out.add(taxon, label, value)
return out
def test_invalid():
w = NexusWriter()
with pytest.raises(ValueError):
w.write()
def test_write_with_no_data_but_trees():
nex = NexusWriter()
nex.trees.append('tree tree1 = (French,(English,Latin));')
content = nex.write()
assert re.search(r"BEGIN TREES", content)
assert re.search(r"tree tree1 = \(French,\(English,Latin\)\);", content)
def setUp(self):
self.nex = NexusWriter()
for char in data:
for taxon, value in data[char].items():
self.nex.add(taxon, char, value)
