def test_mode_accessor():
"""test mode accessor"""
f = nexus(SIMPLE_TEXT, 's')
assert f.mode == 's'
f = nexus(SIMPLE_FILEPATH, 'r')
assert f.mode == 'rU'
def test_iterate():
"""iterate"""
# first, from a string
for entry in nexus(SIMPLE_TEXT, 's'):
assert isinstance(entry, dict)
# next, from a filename
for entry in nexus(SIMPLE_FILEPATH):
assert isinstance(entry, dict)
def test_basic_multi_entry_write():
"""try to write multiple entries"""
entries = [{'name': 'a', 'sequence': 'A'}, {'name': 'g', 'sequence': 'G'}]
f = nexus(os.devnull, 'a')
f.write_entries(entries)
f.close()
def test_read_from_file():
"""read from a filename"""
f = nexus(SIMPLE_FILEPATH, 'r')
entries = f.read()
f.close()
assert 4 == len(entries)
assert isinstance(entries[0], dict)
assert 'Species1' == entries[0]['name']
assert 15 == len(entries[0]['sequence'])
assert isinstance(entries[1], dict)
assert 'Species2' == entries[1]['name']
assert 15 == len(entries[1]['sequence'])
def test_read_from_multiline_file():
"""read from a file where the entries span multiple lines"""
f = nexus(MULTILINE_FILEPATH, 'r')
entries = f.read()
f.close()
assert 2 == len(entries)
assert isinstance(entries[0], dict)
assert 'Species1' == entries[0]['name']
assert 30 == len(entries[0]['sequence'])
assert isinstance(entries[1], dict)
assert 'Species2' == entries[1]['name']
assert 30 == len(entries[1]['sequence'])
def test_read_from_file_handle():
"""read from an open file"""
fh = open(SIMPLE_FILEPATH, 'r')
f = nexus(fh, 'f')
entries = f.readentries()
f.close()
assert 4 == len(entries)
assert isinstance(entries[0], dict)
assert 'Species1' == entries[0]['name']
assert 15 == len(entries[0]['sequence'])
assert isinstance(entries[1], dict)
assert 'Species2' == entries[1]['name']
assert 15 == len(entries[1]['sequence'])
def test_read_from_string():
"""read a string of data"""
# 's' is the 'string' mode
f = nexus(SIMPLE_TEXT, 's')
entries = f.readentries()
f.close()
print entries
assert 4 == len(entries)
assert isinstance(entries[0], dict)
assert 'Species1' == entries[0]['name']
assert 15 == len(entries[0]['sequence'])
assert isinstance(entries[1], dict)
assert 'Species2' == entries[1]['name']
assert 15 == len(entries[1]['sequence'])
def test_bad_value_to_write():
"""try to write entry without name"""
f = nexus(os.devnull, 'a')
f.write({'sequence': 'AGCT'})
f.close()
def test_bad_mode_option():
"""pass non-string to mode option"""
f = nexus(SIMPLE_TEXT, 1)
def test_bad_mode_string():
"""pass unknown mode string"""
f = nexus(SIMPLE_TEXT, 'q')
