def _run(self, _config, temp):
merged_msas = []
for (name, files_dd) in sorted(self._infiles.iteritems()):
partitions = files_dd["partitions"]
msas = dict((key, []) for key in partitions)
for filename in files_dd["filenames"]:
msa = MSA.from_file(filename)
if self._excluded:
msa = msa.exclude(self._excluded)
for (key, msa_part) in msa.split(partitions).iteritems():
msas[key].append(msa_part)
msas.pop("X", None)
for (key, msa_parts) in sorted(msas.iteritems()):
merged_msa = MSA.join(*msa_parts)
if self._reduce:
merged_msa = merged_msa.reduce()
if merged_msa is not None:
merged_msas.append(("%s_%s" % (name, key),
merged_msa))
out_fname_phy = reroot_path(temp, self._out_prefix + ".phy")
with open(out_fname_phy, "w") as output_phy:
final_msa = MSA.join(*(msa for (_, msa) in merged_msas))
output_phy.write(interleaved_phy(final_msa))
partition_end = 0
out_fname_parts = reroot_path(temp, self._out_prefix + ".partitions")
with open(out_fname_parts, "w") as output_part:
for (name, msa) in merged_msas:
length = msa.seqlen()
output_part.write("DNA, %s = %i-%i\n"
% (name,
partition_end + 1,
partition_end + length))
partition_end += length
def _run(self, _config, temp):
merged_msas = []
for (name, files_dd) in sorted(self._infiles.iteritems()):
partitions = files_dd["partitions"]
msas = dict((key, []) for key in partitions)
for filename in files_dd["filenames"]:
msa = MSA.from_file(filename)
if self._excluded:
msa = msa.exclude(self._excluded)
for (key, msa_part) in msa.split(partitions).iteritems():
msas[key].append(msa_part)
msas.pop("X", None)
for (key, msa_parts) in sorted(msas.iteritems()):
merged_msa = MSA.join(*msa_parts)
if self._reduce:
merged_msa = merged_msa.reduce()
if merged_msa is not None:
merged_msas.append(("%s_%s" % (name, key), merged_msa))
out_fname_phy = reroot_path(temp, self._out_prefix + ".phy")
with open(out_fname_phy, "w") as output_phy:
final_msa = MSA.join(*(msa for (_, msa) in merged_msas))
output_phy.write(interleaved_phy(final_msa))
partition_end = 0
out_fname_parts = reroot_path(temp, self._out_prefix + ".partitions")
with open(out_fname_parts, "w") as output_part:
for (name, msa) in merged_msas:
length = msa.seqlen()
output_part.write(
"DNA, %s = %i-%i\n" %
(name, partition_end + 1, partition_end + length))
partition_end += length
def _run(self, _config, temp):
msa = MSA.join(*(MSA.from_file(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))
def _run(self, _config, temp):
msa = MSA.join(*(MSA.from_file(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))
def test_msa_join__missing_arguments():
MSA.join()
def test_msa_join__three_msa():
expected = MSA((FASTA("nc", None, "ACGTGAAAG"),
FASTA("nm", None, "TGACTTGAG"),
FASTA("miRNA", None, "UCAGACCAU")))
result = MSA.join(_JOIN_MSA_1, _JOIN_MSA_2, _JOIN_MSA_3)
assert_equal(result, expected)
def test_msa_join__two_msa():
expected = MSA((FASTA("nc", None, "ACGTGA"),
FASTA("nm", None, "TGACTT"),
FASTA("miRNA", None, "UCAGAC")))
result = MSA.join(_JOIN_MSA_1, _JOIN_MSA_2)
assert_equal(result, expected)
def test_msa_join__single_msa():
result = MSA.join(_JOIN_MSA_1)
assert_equal(result, _JOIN_MSA_1)
