def test_mode_accessor():
"""test mode accessor"""
ff = phylip(SIMPLE_TEXT, 's')
assert ff.mode == 's'
ff = phylip(SIMPLE_FILEPATH, 'r')
assert ff.mode == 'rU'
def test_iterate_phylip():
"""iterate phylip with parsing"""
# first, from a string of phylip data
for entry in phylip(SIMPLE_TEXT, 's'):
assert isinstance(entry, dict)
# next, from a filename with phylip data
for entry in phylip(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'}]
ff = phylip(os.devnull, 'a')
ff.write_entries(entries)
ff.close()
def test_read_phylip_from_file():
"""read phylip given a filename"""
ff = phylip(SIMPLE_FILEPATH, 'r')
entries = ff.read()
ff.close()
assert 10 == len(entries)
assert isinstance(entries[0], dict)
assert 'Cow' == entries[0]['name']
assert 60 == len(entries[0]['sequence'])
assert isinstance(entries[1], dict)
assert 'Carp' == entries[1]['name']
assert 60 == len(entries[1]['sequence'])
def test_read_phylip_from_string():
"""read phylip given a string of phylip data"""
# 's' is the 'string' mode
ff = phylip(SIMPLE_TEXT, 's')
entries = ff.readentries()
ff.close()
print entries
assert 10 == len(entries)
assert isinstance(entries[0], dict)
assert 'Cow' == entries[0]['name']
assert 60 == len(entries[0]['sequence'])
assert isinstance(entries[1], dict)
assert 'Carp' == entries[1]['name']
assert 60 == len(entries[1]['sequence'])
def test_with():
"""test of with statement hooks"""
with phylip(SIMPLE_FILEPATH, 'r') as f:
for entry in f:
assert isinstance(entry, dict)
assert f.closed
def test_bad_value_to_write():
"""try to write entry without name"""
ff = phylip(os.devnull, 'a')
ff.write({'sequence': 'AGCT'})
ff.close()
def test_bad_mode_option():
"""pass non-string to mode option to phylip"""
ff = phylip(SIMPLE_TEXT, 1)
def test_bad_mode_string():
"""pass unknown mode string to phylip"""
ff = phylip(SIMPLE_TEXT, 'q')