def test_write_msa(temp_folder):
msa = {"seq1" : "ACGTA", "seq2" : "CGTAC"}
fname = os.path.join(temp_folder, "out.afa")
with RequiredCall(_VALIDATION_PATH, args = [msa]):
write_msa(msa, fname)
with RequiredCall(_VALIDATION_PATH, args = [msa]):
assert_equal(read_msa(fname), msa)
def test_write_msa(temp_folder):
msa = {"seq1": "ACGTA", "seq2": "CGTAC"}
fname = os.path.join(temp_folder, "out.afa")
with RequiredCall(_VALIDATION_PATH, args=[msa]):
write_msa(msa, fname)
with RequiredCall(_VALIDATION_PATH, args=[msa]):
assert_equal(read_msa(fname), msa)
def test_read_msa__compressed_bz2():
expected = {
"This_is_BZ_FASTA!": "CGTNA",
"This_is_ALSO_BZ_FASTA!": "ACGTN"
}
with RequiredCall(_VALIDATION_PATH, args=[expected]):
results = read_msa("tests/data/fasta_file.fasta.bz2")
assert_equal(results, expected)
def _run(self, _config, temp):
# Read and check that MSAs share groups
msas = [read_msa(filename) for filename in sorted(self.input_files)]
join_msa(*msas)
blocks = []
for msa in msas:
blocks.append(sequential_phy(msa, add_flag = self._add_flag))
with open(reroot_path(temp, self._out_phy), "w") as output:
output.write("\n\n".join(blocks))
def _read_sequences(filenames):
expected_groups = None
for filename in sorted(filenames):
msa = read_msa(filename)
if not expected_groups:
expected_groups = set(msa)
elif set(msa) != expected_groups:
difference = expected_groups.symmetric_difference(msa)
raise NodeError("Unexpected/missing groups for sequence (%s): %s" \
% (filename, ", ".join(difference)))
yield (filename, msa)
def _run(self, _config, temp):
msa = read_msa(self._input_file)
for excluded_group in self._excluded:
msa.pop(excluded_group)
lines = []
lines.append(" %i %i" % (len(msa), len(msa.itervalues().next())))
for (name, seq) in sorted(msa.iteritems()):
lines.append("")
lines.append(name)
for line in fragment(60, seq.upper()):
lines.append(" ".join(fragment(3, line)))
with open(fileutils.reroot_path(temp, self._output_file), "w") as output:
output.write("\n".join(lines))
def _run(self, _config, temp):
alignment = msa.read_msa(self._input_file)
for (to_filter, groups) in self._filter_by.iteritems():
sequences = [alignment[group] for group in groups]
sequence = list(alignment[to_filter])
for (index, nts) in enumerate(zip(*sequences)):
nt = sequence[index]
if (nt not in "Nn-") and (nts.count(nt) == 1):
sequence[index] = 'n'
alignment[to_filter] = "".join(sequence)
temp_filename = fileutils.reroot_path(temp, self._output_file)
msa.write_msa(alignment, temp_filename)
fileutils.move_file(temp_filename, self._output_file)
def _run(self, _config, temp):
alignment = msa.read_msa(self._input_file)
for (to_filter, groups) in self._filter_by.iteritems():
sequences = [alignment[group] for group in groups]
sequence = list(alignment[to_filter])
for (index, nts) in enumerate(zip(*sequences)):
nt = sequence[index]
if (nt not in "Nn-") and (nts.count(nt) == 1):
sequence[index] = 'n'
alignment[to_filter] = "".join(sequence)
temp_filename = fileutils.reroot_path(temp, self._output_file)
msa.write_msa(alignment, temp_filename)
fileutils.move_file(temp_filename, self._output_file)
def _run(self, _config, temp):
msa = read_msa(self._input_file)
for excluded_group in self._excluded:
msa.pop(excluded_group)
lines = []
lines.append(" %i %i" % (len(msa), len(msa.itervalues().next())))
for (name, seq) in sorted(msa.iteritems()):
lines.append("")
lines.append(name)
for line in fragment(60, seq.upper()):
lines.append(" ".join(fragment(3, line)))
with open(fileutils.reroot_path(temp, self._output_file),
"w") as output:
output.write("\n".join(lines))
def _run(self, _config, temp):
msas = []
for filename in sorted(self._infiles):
split_by = self._infiles[filename].get("partition_by", self._part_by)
for (key, msa) in sorted(split_msa(read_msa(filename), split_by).items()):
for excluded_group in self._excluded:
msa.pop(excluded_group)
msas.append(("%s_%s" % (self._infiles[filename]["name"], key), msa))
msa = join_msa(*(msa for (_, msa) in msas))
with open(reroot_path(temp, self._out_prefix + ".phy"), "w") as output:
output.write(interleaved_phy(msa, add_flag = self._add_flag))
with open(reroot_path(temp, self._out_prefix + ".partitions"), "w") as output:
end = 0
for (name, msa) in msas:
length = len(msa.itervalues().next())
output.write("DNA, %s = %i-%i\n" % (name, end + 1, end + length))
end += length
def test_read_msa__compressed_bz2():
expected = {"This_is_BZ_FASTA!" : "CGTNA",
"This_is_ALSO_BZ_FASTA!" : "ACGTN"}
with RequiredCall(_VALIDATION_PATH, args = [expected]):
results = read_msa("tests/data/fasta_file.fasta.bz2")
assert_equal(results, expected)
def _run(self, _config, temp):
msa = join_msa(*(read_msa(filename) for filename in sorted(self.input_files)))
with open(reroot_path(temp, self._out_phy), "w") as output:
output.write(interleaved_phy(msa, add_flag = self._add_flag))