def interleaved_phy(msa, add_flag=False, max_name_length=_MAX_NAME_LENGTH):
validate_msa(msa)
header = "%i %i" % (len(msa), len(msa.values()[0]))
if add_flag:
header += " I"
result = [header, ""]
padded_len = min(max_name_length, max(len(name) for name in msa)) + 2
padded_len -= padded_len % -(_BLOCK_SIZE + _BLOCK_SPACING) + _BLOCK_SPACING
streams = []
spacing = " " * _BLOCK_SPACING
for (name, sequence) in sorted(msa.iteritems()):
name = name[:max_name_length]
padding = (padded_len - len(name)) * " "
lines = []
line = [name, padding]
for block in grouper(_BLOCK_SIZE, 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 interleaved_phy(msa, add_flag = False, max_name_length = _MAX_NAME_LENGTH):
validate_msa(msa)
header = "%i %i" % (len(msa), len(msa.values()[0]))
if add_flag:
header += " I"
result = [header, ""]
padded_len = min(max_name_length, max(len(name) for name in msa)) + 2
padded_len -= padded_len % -(_BLOCK_SIZE + _BLOCK_SPACING) + _BLOCK_SPACING
streams = []
spacing = " " * _BLOCK_SPACING
for (name, sequence) in sorted(msa.iteritems()):
name = name[:max_name_length]
padding = (padded_len - len(name)) * " "
lines = []
line = [name, padding]
for block in grouper(_BLOCK_SIZE, 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 sequential_phy(msa, add_flag = False, max_name_length = _MAX_NAME_LENGTH):
validate_msa(msa)
header = "%i %i" % (len(msa), len(msa.values()[0]))
if add_flag:
header += " S"
spacing = " " * _BLOCK_SPACING
result = [header, ""]
for (name, sequence) in sorted(msa.iteritems()):
result.append(name[:max_name_length])
blocks = grouper(_BLOCK_SIZE, 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 test_grouper__non_empty_list_with_trailing_fill_value():
result = utils.grouper(3, range(7), fillvalue=r'\0')
expected = [(0, 1, 2), (3, 4, 5), (6, r'\0', r'\0')]
assert_equal(list(result), expected)
def test_grouper__non_empty_list_with_trailing():
result = utils.grouper(3, range(7))
expected = [(0, 1, 2), (3, 4, 5), (6, None, None)]
assert_equal(list(result), expected)
def test_grouper__non_empty_list():
result = utils.grouper(3, range(6))
expected = [(0, 1, 2), (3, 4, 5)]
assert_equal(list(result), expected)
def test_grouper__empty_list():
result = utils.grouper(3, [])
assert_equal(list(result), [])
def test_grouper__non_empty_list_with_trailing_fill_value():
result = utils.grouper(3, range(7), fillvalue = r'\0')
expected = [(0, 1, 2), (3, 4, 5), (6, r'\0', r'\0')]
assert_equal(list(result), expected)
def test_grouper__non_empty_list_with_trailing():
result = utils.grouper(3, range(7))
expected = [(0, 1, 2), (3, 4, 5), (6, None, None)]
assert_equal(list(result), expected)
def test_grouper__non_empty_list():
result = utils.grouper(3, range(6))
expected = [(0, 1, 2), (3, 4, 5)]
assert_equal(list(result), expected)
def test_grouper__empty_list():
result = utils.grouper(3, [])
assert_equal(list(result), [])