def test_one_and_four(self):
"""Tests combining two non-zero lists"""
one_seq_file = os.path.join(data_dir, 'Hsap_AP1G_OneSeq.fa')
four_seqs_file = os.path.join(data_dir, 'Hsap_AP1G_FourSeqs.fa')
one_record = sequence_file._get_sequences(one_seq_file)
four_records = sequence_file._get_sequences(four_seqs_file)
self.assertEqual(
len(sequence_file._cat_sequence_lists(one_record, four_records)),
5)
def setUp(self):
"""Makes a temporary directory in 'tests/fixtures'"""
self.tmpdir = os.path.join(data_dir, 'tmp')
try:
os.makedirs(self.tmpdir)
except FileExistsError:
pass # already made
self.one_seq_file = os.path.join(data_dir, 'Hsap_AP1G_OneSeq.fa')
self.four_seqs_file = os.path.join(data_dir, 'Hsap_AP1G_FourSeqs.fa')
self.one_record = sequence_file._get_sequences(self.one_seq_file)
self.four_records = sequence_file._get_sequences(self.four_seqs_file)
self.cat_list = sequence_file._cat_sequence_lists(
self.one_record, self.four_records)
def _parse_infiles(self):
"""Reads infiles to create ScrollSeq objects.
Assumes that the input files have already been checked and are
appropriate (no duplicates/empty/non-existent files).
Args:
(self.infiles)
Returns:
modifies internal _seq_dict and _groups variables
"""
for file_path in self.infiles:
group = os.path.basename(file_path).split('.', 1)[0]
if not len(group) > 0: # This should never happen in reality
group = str(self._group_counter)
self._group_counter += 1
assert isinstance(group, str)
# Files are unique, but need to check groups; two different
# filepaths could lead to the same group name
group = self._unique_group_name(group)
# Now get SeqRecords using BioPython
records = sf._get_sequences(
file_path,
self._file_format,
)
scroll_seqs = self._make_scroll_seqs(
file_path,
group,
records,
)
# Update internal objects
self._groups.append(group)
self._seq_dict[group] = scroll_seqs
def setUp(self):
"""Creates a new ScrollCollection Object"""
# Populate ARGS values of config file
load_config_file()
try:
config.add_section('ARGS')
except DuplicateSectionError:
pass
# Now provide sufficient arg defaults
config['ARGS']['filter'] = 'False'
config['ARGS']['filter_method'] = 'zscore'
config['ARGS']['dist_matrix'] = 'LG'
config['ARGS']['no_clobber'] = 'True'
ids = (1, 2, 3, 4)
infile = os.path.join(data_dir, 'Hsap_AP1G_FourSeqs.fa')
records = sf._get_sequences(infile)
self.seq_list = []
for id_num, seq_record in zip(ids, records):
self.seq_list.append(
ScrollSeq(
id_num, # ID
infile, # infile
id_num, # Group; not important here
SeqRecord=seq_record))
self.tmpdir = os.path.join(data_dir, 'tmp')
try:
os.makedirs(self.tmpdir)
except FileExistsError:
pass # tmpdir still present
self.collection = ScrollCollection(
self.tmpdir, # outdir
self.seq_list, # sequence list
'one', # group
'Mafft', # align_method
'RAxML', # dist_method
)
def test_four_sequences(self):
"""Tests that parsing four sequences works fine."""
four_seqs_file = os.path.join(data_dir, 'Hsap_AP1G_FourSeqs.fa')
records = sequence_file._get_sequences(four_seqs_file)
self.assertEqual(len(records), 4)
def test_one_sequence(self):
"""Tests that parsing one sequence works fine."""
one_seq_file = os.path.join(data_dir, 'Hsap_AP1G_OneSeq.fa')
records = sequence_file._get_sequences(one_seq_file)
self.assertEqual(len(records), 1)