def test_repeated_names_with_taxa(self):
# TODO - remove these prints, check output explicitly
print("Repeated names with a TAXA block")
handle = StringIO("""#NEXUS
[TITLE: NoName]
begin taxa
CYS1_DICDI
ALEU_HORVU
CATH_HUMAN
CYS1_DICDI;
end;
begin data;
dimensions ntax=4 nchar=50;
format interleave datatype=protein gap=- symbols="FSTNKEYVQMCLAWPHDRIG";
matrix
CYS1_DICDI -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ----
ALEU_HORVU MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG
CATH_HUMAN ------MWAT LPLLCAGAWL LGV------- -PVCGAAELS VNSLEK----
CYS1_DICDI -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---X
;
end;
""") # noqa : W291
for a in NexusIterator(handle):
print(a)
for r in a:
print("%r %s %s" % (r.seq, r.name, r.id))
print("Done")
def test_repeated_names_with_taxa(self):
print("Repeated names with a TAXA block")
handle = StringIO("""#NEXUS
[TITLE: NoName]
begin taxa
CYS1_DICDI
ALEU_HORVU
CATH_HUMAN
CYS1_DICDI;
end;
begin data;
dimensions ntax=4 nchar=50;
format interleave datatype=protein gap=- symbols="FSTNKEYVQMCLAWPHDRIG";
matrix
CYS1_DICDI -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ----
ALEU_HORVU MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG
CATH_HUMAN ------MWAT LPLLCAGAWL LGV------- -PVCGAAELS VNSLEK----
CYS1_DICDI -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---X
;
end;
""") # noqa for pep8 W291 trailing whitespace
for a in NexusIterator(handle):
print(a)
for r in a:
print("%r %s %s" % (r.seq, r.name, r.id))
print("Done")
def test_empty_file(self):
print("Reading an empty file")
assert 0 == len(list(NexusIterator(StringIO())))
print("Done")
print("")
print("Writing...")
handle = StringIO()
NexusWriter(handle).write_file([a])
handle.seek(0)
print(handle.read())
handle = StringIO()
try:
NexusWriter(handle).write_file([a, a])
assert False, "Should have rejected more than one alignment!"
except ValueError:
pass
def test_empty_file(self):
print("Reading an empty file")
assert 0 == len(list(NexusIterator(StringIO())))
print("Done")
print("")
print("Writing...")
handle = StringIO()
NexusWriter(handle).write_file([a])
handle.seek(0)
print(handle.read())
handle = StringIO()
try:
NexusWriter(handle).write_file([a, a])
assert False, "Should have rejected more than one alignment!"
except ValueError:
pass
def test_empty_file_read(self):
self.assertEqual([], list(NexusIterator(StringIO())))
