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"""
Support for the `MAF`_ multiple sequence alignment format used by `multiz`_.
.. _MAF: http://genome.ucsc.edu/FAQ/FAQformat.html#format5
.. _multiz: http://www.bx.psu.edu/miller_lab/
"""
from io import (
StringIO,
TextIOWrapper,
)
from bx import interval_index_file
from bx.align import (
Alignment,
Component,
)
MAF_INVERSE_STATUS = "V"
MAF_INSERT_STATUS = "I"
MAF_CONTIG_STATUS = "C"
MAF_CONTIG_NESTED_STATUS = "c"
MAF_NEW_STATUS = "N"
MAF_NEW_NESTED_STATUS = "n"
MAF_MAYBE_NEW_STATUS = "S"
MAF_MAYBE_NEW_NESTED_STATUS = "s"
MAF_MISSING_STATUS = "M"
class MAFIndexedAccess(interval_index_file.AbstractIndexedAccess):
"""
Indexed access to a MAF file.
"""
def read_at_current_offset(self, file, **kwargs):
"""
Read the MAF block at the current position in `file` and return an
instance of `Alignment`.
"""
return read_next_maf(file, **kwargs)
def open_data(self):
data = super().open_data()
return TextIOWrapper(data, encoding="ascii")
class MAFMultiIndexedAccess(interval_index_file.AbstractMultiIndexedAccess):
"""
Indexed access to multiple MAF files.
"""
indexed_access_class = MAFIndexedAccess
Indexed = MAFIndexedAccess
"""Deprecated: `MAFIndexedAccess` is also available under the name `Indexed`."""
MultiIndexed = MAFMultiIndexedAccess
"""Deprecated: `MAFMultiIndexedAccess` is also available under the name `MultiIndexed`."""
class Reader:
"""
Iterate over all maf blocks in a file in order
"""
def __init__(self, file, **kwargs):
self.file = file
self.maf_kwargs = kwargs
# Read and verify maf header, store any attributes
fields = self.file.readline().split()
if fields[0] != "##maf":
raise Exception("File does not have MAF header")
self.attributes = parse_attributes(fields[1:])
def __next__(self):
return read_next_maf(self.file, **self.maf_kwargs)
def __iter__(self):
return ReaderIter(self)
def close(self):
self.file.close()
class ReaderIter:
"""
Adapts a `Reader` to the iterator protocol.
"""
def __init__(self, reader):
self.reader = reader
def __iter__(self):
return self
def __next__(self):
v = next(self.reader)
if not v:
raise StopIteration
return v
class Writer:
def __init__(self, file, attributes=None):
if attributes is None:
attributes = {}
self.file = file
# Write header, Webb's maf code wants version first, we accomodate
if "version" not in attributes:
attributes["version"] = 1
self.file.write("##maf version={}".format(attributes["version"]))
for key in attributes:
if key == "version":
continue
self.file.writelines(f" {key}={attributes[key]}")
self.file.write("\n")
def write(self, alignment):
self.file.write("a score=" + str(alignment.score))
for key in alignment.attributes:
self.file.write(f" {key}={alignment.attributes[key]}")
self.file.write("\n")
# Components
rows = []
for c in alignment.components:
# "Empty component" generates an 'e' row
if c.empty:
rows.append(("e", c.src, str(c.start), str(c.size), c.strand, str(c.src_size), c.synteny_empty))
continue
# Regular component
rows.append(("s", c.src, str(c.start), str(c.size), c.strand, str(c.src_size), c.text))
# If component has quality, write a q row
if c.quality is not None:
rows.append(("q", c.src, "", "", "", "", c.quality))
# If component has synteny follow up with an 'i' row
if c.synteny_left and c.synteny_right:
rows.append(("i", c.src, "", "", "", "", " ".join(map(str, c.synteny_left + c.synteny_right))))
self.file.write(format_tabular(rows, "llrrrrl"))
self.file.write("\n")
def close(self):
self.file.close()
# ---- Helper methods -------------------------------------------------------
def from_string(string, **kwargs):
return read_next_maf(StringIO(string), **kwargs)
def read_next_maf(file, species_to_lengths=None, parse_e_rows=False):
"""
Read the next MAF block from `file` and return as an `Alignment`
instance. If `parse_e_rows` is true, empty components will be created
when e rows are encountered.
"""
alignment = Alignment(species_to_lengths=species_to_lengths)
# Attributes line
line = readline(file, skip_blank=True)
if not line:
return None
fields = line.split()
if fields[0] != "a":
raise Exception("Expected 'a ...' line")
alignment.attributes = parse_attributes(fields[1:])
if "score" in alignment.attributes:
alignment.score = alignment.attributes["score"]
del alignment.attributes["score"]
else:
alignment.score = 0
# Sequence lines
last_component = None
while True:
line = readline(file)
# EOF or Blank line terminates alignment components
if not line or line.isspace():
break
if line.isspace():
break
# Parse row
fields = line.split()
if fields[0] == "s":
# An 's' row contains sequence for a component
component = Component()
component.src = fields[1]
component.start = int(fields[2])
component.size = int(fields[3])
component.strand = fields[4]
component.src_size = int(fields[5])
if len(fields) > 6:
component.text = fields[6].strip()
# Add to set
alignment.add_component(component)
last_component = component
elif fields[0] == "e":
# An 'e' row, when no bases align for a given species this tells
# us something about the synteny
if parse_e_rows:
component = Component()
component.empty = True
component.src = fields[1]
component.start = int(fields[2])
component.size = int(fields[3])
component.strand = fields[4]
component.src_size = int(fields[5])
component.text = None
synteny = fields[6].strip()
assert len(synteny) == 1, "Synteny status in 'e' rows should be denoted with a single character code"
component.synteny_empty = synteny
alignment.add_component(component)
last_component = component
elif fields[0] == "i":
# An 'i' row, indicates left and right synteny status for the
# previous component, we hope ;)
assert fields[1] == last_component.src, "'i' row does not follow matching 's' row"
last_component.synteny_left = (fields[2], int(fields[3]))
last_component.synteny_right = (fields[4], int(fields[5]))
elif fields[0] == "q":
assert fields[1] == last_component.src, "'q' row does not follow matching 's' row"
# TODO: Should convert this to an integer array?
last_component.quality = fields[2]
return alignment
def readline(file, skip_blank=False):
"""Read a line from provided file, skipping any blank or comment lines"""
while True:
line = file.readline()
if not line:
return None
if line[0] != "#" and not (skip_blank and line.isspace()):
return line
def parse_attributes(fields):
"""Parse list of key=value strings into a dict"""
attributes = {}
for field in fields:
pair = field.split("=")
attributes[pair[0]] = pair[1]
return attributes
def format_tabular(rows, align=None):
if len(rows) == 0:
return ""
lengths = [len(col) for col in rows[0]]
for row in rows[1:]:
for i in range(0, len(row)):
lengths[i] = max(lengths[i], len(row[i]))
rval = ""
for row in rows:
for i in range(0, len(row)):
if align and align[i] == "l":
rval += row[i].ljust(lengths[i])
else:
rval += row[i].rjust(lengths[i])
rval += " "
rval += "\n"
return rval
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