def test_valid_no_headers(self):
"""Test the function with valid Sequences and no variable headers.
"""
seq1 = Sequence(name='seq1')
seq1.set_cont_values([1.0, 2.0, 3.0])
seq2 = Sequence(name='seq2')
seq2.set_cont_values([3.0, 3.2, 4.1])
test_sequence_list = [seq1, seq2]
mtx = dr.get_character_matrix_from_sequences_list(test_sequence_list)
assert isinstance(mtx, Matrix)
def test_valid_with_headers(self):
"""Test the function with valid Sequences and include headers.
"""
seq1 = Sequence(name='seq1')
seq1.set_cont_values([1.0, 2.0, 3.0])
seq2 = Sequence(name='seq2')
seq2.set_cont_values([3.0, 3.2, 4.1])
test_sequence_list = [seq1, seq2]
col_headers = ['Val 1', 'Val 2', 'Val 3']
mtx = dr.get_character_matrix_from_sequences_list(
test_sequence_list, var_headers=col_headers)
assert isinstance(mtx, Matrix)
assert mtx.get_column_headers() == col_headers
def create_sequence_list_from_dict(values_dict):
"""Creates a list of sequences from a dictionary
Args:
values_dict (dict) : A dictionary of taxon name keys and a list of
values for each value.
Note:
* The dictionary should have structure::
{
"{taxon_name}" : [{values}]
}
Returns:
A list of Sequence objects and None for headers.
Raises:
AlignmentIOError: If a dictionary value is not a list.
"""
headers = None
sequence_list = []
for name, values in values_dict.items():
if not isinstance(values, list):
raise AlignmentIOError('Values must be a list')
seq = Sequence(name=name)
seq.set_cont_values(values)
sequence_list.append(seq)
return sequence_list, headers
def read_table_alignment_flo(table_flo):
"""Reads a table from a file-like object.
Args:
table_flo (file-like): A file-like object containing table data.
Returns:
A list of Sequence objects.
Raises:
AlignmentIOError: If there is a problem creating sequences.
"""
seqlist = []
for i in table_flo:
if len(i) > 2:
try:
spls = i.strip().split("\t")
name = spls[0].strip()
seq = spls[1].strip().split(" ")
seq = [float(j) for j in seq]
tseq = Sequence(name=name)
tseq.set_cont_values(seq)
seqlist.append(tseq)
except Exception as e:
raise AlignmentIOError(str(e))
return seqlist
def read_json_alignment_flo(json_flo):
"""Read a JSON file-like object and return a list of sequences and headers.
Args:
json_flo (file-like): A file-like object with JSON alignment data.
Note:
* File should have structure::
{
"headers" : [{header_names}],
"values" : [
{
"name" : "{taxon_name}",
"values" : [{values}]
}
]
}
Returns:
A list of Sequence objects and headers.
Raises:
AlignmentIOError: If headers are provided but they are not a list.
"""
json_vals = json.load(json_flo)
if 'headers' in json_vals.keys():
headers = json_vals['headers']
if not isinstance(headers, list):
raise AlignmentIOError(
'If headers are provided, they must be a list')
else:
headers = None
sequence_list = []
for val_dict in json_vals['values']:
name = val_dict['name']
vals = [float(v) for v in val_dict['values']]
seq = Sequence(name=name)
seq.set_cont_values(vals)
sequence_list.append(seq)
return sequence_list, headers
def read_phylip_alignment_flo(phylip_flo):
"""Reads a phylip alignment file-like object and return the sequences.
Args:
phylip_flo (file-like): The phylip file-like object.
Note:
* We assume that the phylip files are extended and not strict (in terms
of how many characters for taxon names).
* The phylip file is in the format::
numoftaxa numofsites
seqlabel sequence
seqlabel sequence
Returns:
A list of Sequence objects.
Raises:
AlignmentIOError: If there is a problem creating sequences.
"""
seqlist = []
# first line is the number of taxa and num of sites
# we don't really even need to read this line,
# so let's just skip it
i = phylip_flo.readline()
for i in phylip_flo:
try:
if len(i) > 2:
spls = i.strip().split()
name = spls[0].strip()
seq = spls[1].strip()
tseq = Sequence(name=name, seq=seq)
seqlist.append(tseq)
except Exception as e:
raise AlignmentIOError(str(e))
return seqlist
def read_csv_alignment_flo(csv_flo):
"""Reads a CSV file-like object and return a list of sequences and headers.
Args:
csv_flo (file-like): A file-like object with CSV alignment data.
Returns:
A list of Sequence objects and headers.
Raises:
AlignmentIOError: If the number of columns is inconsistent across the
sequences.
"""
headers = None
sequence_list = []
has_header = csv.Sniffer().has_header(csv_flo.readline())
csv_flo.seek(0)
num_parts = None
for line in csv_flo:
parts = line.strip().split(',')
if num_parts is None:
num_parts = len(parts)
else:
if len(parts) != num_parts:
raise AlignmentIOError('Number of columns is inconsistent')
if has_header and headers is None:
headers = parts[1:]
else:
name = parts[0]
vals = [float(i) for i in parts[1:]]
seq = Sequence(name=name)
seq.set_cont_values(vals)
sequence_list.append(seq)
return sequence_list, headers