def interleaved_phy(msa, add_flag = False, max_name_length = _MAX_NAME_LENGTH):
MSA.validate(msa)
header = "%i %i" % (len(msa), msa.seqlen())
if add_flag:
header += " I"
result = [header, ""]
padded_len = min(max_name_length, max(len(name) for name in msa.names())) + 2
padded_len -= padded_len % -(_BLOCK_SIZE + _BLOCK_SPACING) + _BLOCK_SPACING
streams = []
spacing = " " * _BLOCK_SPACING
for record in sorted(msa):
name = record.name[:max_name_length]
padding = (padded_len - len(name)) * " "
lines = []
line = [name, padding]
for block in grouper(_BLOCK_SIZE, record.sequence, fillvalue = ""):
block = "".join(block)
if sum(len(segment) for segment in line) >= _LINE_SIZE:
lines.append("".join(line))
line = [block]
else:
line.extend((spacing, block))
lines.append("".join(line))
streams.append(lines)
for rows in zip(*streams):
result.extend(row for row in rows)
result.append("")
result.pop()
return "\n".join(result)
def _read_sequences(filenames):
results = {}
for filename in filenames:
results[filename] = MSA.from_file(filename)
MSA.validate(*results.values())
return results.iteritems()
def _read_sequences(filenames):
results = {}
for filename in filenames:
results[filename] = MSA.from_file(filename)
MSA.validate(*results.values())
return results.iteritems()
def _run(self, _config, temp):
# Read and check that MSAs share groups
msas = [MSA.from_file(filename) for filename in sorted(self.input_files)]
MSA.validate(*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 _run(self, _config, temp):
# Read and check that MSAs share groups
msas = [
MSA.from_file(filename) for filename in sorted(self.input_files)
]
MSA.validate(*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 sequential_phy(msa, add_flag = False, max_name_length = _MAX_NAME_LENGTH):
MSA.validate(msa)
header = "%i %i" % (len(msa), msa.seqlen())
if add_flag:
header += " S"
spacing = " " * _BLOCK_SPACING
result = [header, ""]
for record in sorted(msa):
result.append(record.name[:max_name_length])
blocks = grouper(_BLOCK_SIZE, record.sequence, fillvalue = "")
lines = grouper(_NUM_BLOCKS, blocks)
for line in lines:
result.append(spacing.join("".join(block) for block in line if block))
return "\n".join(result)
def sequential_phy(msa, add_flag=False, max_name_length=_MAX_NAME_LENGTH):
MSA.validate(msa)
header = "%i %i" % (len(msa), msa.seqlen())
if add_flag:
header += " S"
spacing = " " * _BLOCK_SPACING
result = [header, ""]
for record in sorted(msa):
result.append(record.name[:max_name_length])
blocks = grouper(_BLOCK_SIZE, record.sequence, fillvalue="")
lines = grouper(_NUM_BLOCKS, blocks)
for line in lines:
result.append(
spacing.join("".join(block) for block in line if block))
return "\n".join(result)
def interleaved_phy(msa, add_flag=False, max_name_length=_MAX_NAME_LENGTH):
MSA.validate(msa)
header = "%i %i" % (len(msa), msa.seqlen())
if add_flag:
header += " I"
result = [header, ""]
padded_len = min(max_name_length, max(len(name)
for name in msa.names())) + 2
padded_len -= padded_len % -(_BLOCK_SIZE + _BLOCK_SPACING) + _BLOCK_SPACING
streams = []
spacing = " " * _BLOCK_SPACING
for record in sorted(msa):
name = record.name[:max_name_length]
padding = (padded_len - len(name)) * " "
lines = []
line = [name, padding]
for block in grouper(_BLOCK_SIZE, record.sequence, fillvalue=""):
block = "".join(block)
if sum(len(segment) for segment in line) >= _LINE_SIZE:
lines.append("".join(line))
line = [block]
else:
line.extend((spacing, block))
lines.append("".join(line))
streams.append(lines)
for rows in zip(*streams):
result.extend(row for row in rows)
result.append("")
result.pop()
return "\n".join(result)