def __init__(self, data, vlevel=1, virtual=False, version=None):
self.vlevel = vlevel
self._virtual = virtual
self._datatype = {}
self._data = {}
self._gfa = None
self._version = version
self._refs = {}
if self.__class__ == gfapy.Line:
raise gfapy.AssertionError("Line subclass unknown")
if isinstance(data, dict):
# API private initialization using dict
self._data.update(data)
else:
# public initialization using list (or tab-separated string)
if self.__class__ == gfapy.line.Comment:
data = gfapy.Line._init_comment_data(data)
elif isinstance(data, str):
data = data.split(gfapy.Line.SEPARATOR)
if self.version is None:
self._compute_version(data[0])
else:
self._validate_version()
self._initialize_positional_fields(data)
self._initialize_tags(data)
if self.vlevel >= 1:
self._validate_record_type_specific_info()
if self.version is None:
raise gfapy.RuntimeError(
"version could not be determined, " +
"record_type={}".format(self.record_type))
def _remove_junctions(self, jntag):
if jntag is None:
jntag = "jn"
for s in self.segments:
jndata = s.get(jntag)
if jndata:
ln = len(s.sequence)
for m1, dir1 in jndata["L"].items():
for m2, dir2 in jndata["R"].items():
if self._version == "gfa1":
l = gfapy.line.edge.Link([m1,dir1,m2,dir2,"{}M".format(ln)])
self.add_line(l)
elif self._version == "gfa2":
m1ln = len(self.segment(m1).sequence)
m2ln = len(self.segment(m2).sequence)
r1 = (dir1 == "-")
r2 = (dir2 == "-")
l = gfapy.line.edge.GFA2(["*", m1+dir1, m2+dir2,
"0" if r1 else str(m1ln-ln),
str(ln) if r1 else str(m1ln)+"$",
"0" if r2 else str(m2ln-ln),
str(ln) if r1 else str(m2ln)+"$",
str(ln)+"M"])
self.add_line(l)
else:
raise gfapy.AssertionError()
s.disconnect()
def _link_duplicated_last(self, merged, last, is_reversed, jntag):
# annotate junction
if jntag is None:
jntag = "jn"
if not last.get(jntag):
last.set(jntag, {"L":[],"R":[]})
if is_reversed:
last.get(jntag)["R"].append([merged.name, "-"])
else:
last.get(jntag)["L"].append([merged.name, "+"])
# create temporary link
ln = len(last.sequence)
if self._version == "gfa1":
tmp_link = gfapy.line.edge.Link([merged.name, "+",
last.name, "-" if is_reversed else "+",
"{}M".format(ln), "co:Z:temporary"])
self.add_line(tmp_link)
elif self._version == "gfa2":
mln = len(merged.sequence)
tmp_link = gfapy.line.edge.GFA2(["*",merged.name+"+", \
last_name+("-" if is_reversed else "+"),
str(mln - ln), "{}$".format(mln),
str(ln-1) if is_reversed else "0", # on purpose fake
"{}$".format(ln) if is_reversed else "1", # on purpose fake
"{}M".format(ln), "co:Z:temporary"])
self.add_line(tmp_link)
else:
raise gfapy.AssertionError()
def add_line(self, gfa_line):
"""Add a line to a GFA instance.
Note:
append() is an alias to this method
Parameters:
gfa_line (str, Line): a line instance or a string, containing a line
of a GFA file (if a string, a line instance is constructed using
the string)
Raises:
gfapy.error.VersionError : If a wrong line type is used, for the GFA
version
gfapy.error.FormatError : If the content of the line string is
not valid
"""
if gfa_line is None:
return
if self._version == "gfa1":
self.__add_line_GFA1(gfa_line)
elif self._version == "gfa2":
self.__add_line_GFA2(gfa_line)
elif self._version is None:
self.__add_line_unknown_version(gfa_line)
else:
raise gfapy.AssertionError("This point should never be reached")
def __add_line_GFA1(self, gfa_line):
if isinstance(gfa_line, str):
if gfa_line[0] == "S":
gfa_line = gfapy.Line(gfa_line, vlevel=self._vlevel)
else:
gfa_line = gfapy.Line(gfa_line,
vlevel=self._vlevel,
version="gfa1")
elif gfa_line.__class__ in gfapy.Lines.GFA2Specific:
raise gfapy.VersionError(
"Version: 1.0 ({})\n".format(self._version_explanation) +
"Cannot add instance of incompatible line type " +
str(type(gfa_line)))
if gfa_line.record_type == "H":
if self._vlevel > 0 and gfa_line.VN and gfa_line.VN != "1.0":
raise gfapy.VersionError(
"Header line specified wrong version ({})\n".format(
gfa_line.VN) + "Line: {}\n".format(gfa_line) +
"File version: 1.0 ({})".format(self._version_explanation))
self.header._merge(gfa_line)
elif gfa_line.record_type == "S":
if gfa_line.version == "gfa2":
raise gfapy.VersionError(
"Version: 1.0 ({})\n".format(self._version_explanation) +
"GFA2 segment found: {}".format(gfa_line))
gfa_line.connect(self)
elif gfa_line.record_type in ["L", "P", "C", "#"]:
gfa_line.connect(self)
else:
raise gfapy.AssertionError(
"Invalid record type {}. This should never happen".format(rt))
def _backreference_keys(self, ref, key_in_ref):
if ref.record_type == "U":
return ["sets"]
elif ref.record_type == "O":
return ["paths"]
elif ref.record_type == "S":
return ["sid1", "sid2"]
else:
raise gfapy.AssertionError("Bug found, please report\n" +
"ref: {}\n".format(ref) +
"key_in_ref: {}".format(key_in_ref))
def _push_item_on_se_path(self, path, prev_edge, item):
if isinstance(item.line, str):
raise gfapy.RuntimeError(
"Captured path cannot be computed; a reference has not been resolved\n"
+ "Line: {}\n".format(self) +
"Unresolved reference: {} (String found)".format(item.line))
elif isinstance(item.line, gfapy.line.segment.GFA2):
if not item.line.is_connected():
raise gfapy.RuntimeError(
"Captured path cannot be computed; item is not connected\n"
+ "Line: {}\n".format(self) + "Item: {}".format(item.line))
self._push_segment_on_se_path(path, prev_edge, item)
prev_edge = False
elif isinstance(item.line, gfapy.line.edge.GFA2):
if not item.line.is_connected():
raise gfapy.RuntimeError(
"Captured path cannot be computed; item is not connected\n"
+ "Line: {}\n".format(self) + "Item: {}".format(item.line))
if not path:
self._push_first_edge_on_se_path(path, self.items)
else:
self._push_nonfirst_edge_on_se_path(path, item)
prev_edge = True
elif isinstance(item.line, gfapy.line.group.Ordered):
if not item.line.is_connected():
raise gfapy.RuntimeError(
"Captured path cannot be computed; item is not connected\n"
+ "Line: {}\n".format(self) + "Item: {}".format(item.line))
subpath, prev_edge_subpath = item.line._compute_captured_path()
if not subpath:
raise gfapy.AssertionError()
if item.orient == "+":
for subpath_item in subpath:
path, prev_edge = self._push_item_on_se_path(
path, prev_edge, subpath_item)
else:
for subpath_item in reversed(subpath):
path, prev_edge = self._push_item_on_se_path(
path, prev_edge, subpath_item.inverted())
prev_edge = prev_edge_subpath
elif isinstance(item.line, gfapy.line.unknown.Unknown):
raise gfapy.RuntimeError(
"Captured path cannot be computed; a reference has not been resolved\n"
+ "Line: {}\n".format(self) +
"Unresolved reference: {} (Virtual unknown line)".format(
item.name))
else:
raise gfapy.TypeError("Line: {}\t".format(self) +
"Cannot compute captured path:\t" +
"Error: items of type {} are not supported\t"
.format(item.line.__class__.__name__) +
"Unsupported item: {}".format(item))
return path, prev_edge
def _refkey_for_s(self, snum):
a = [self.sid1.orient, self.sid2.orient]
if a == ["+", "+"]:
return "gaps_R" if (snum == 1) else "gaps_L"
elif a == ["+", "-"]:
return "gaps_R"
elif a == ["-", "+"]:
return "gaps_L"
elif a == ["-", "-"]:
return "gaps_L" if (snum == 1) else "gaps_R"
else:
raise gfapy.AssertionError("Bug found, please report\n" +
"snum: {}".format(snum))
def _push_segment_on_se_path(self, path, prev_edge, oriented_segment):
if path:
if isinstance(path[-1].line, gfapy.line.segment.GFA2):
if prev_edge:
self._check_s_is_as_expected(path, oriented_segment)
return # do not add segment, as it is already there
else:
path.append(
self._find_edge_from_path_to_segment(
path, oriented_segment))
elif isinstance(path[-1].line, gfapy.line.edge.GFA2):
self._check_s_to_e_contiguity(path, oriented_segment)
else:
raise gfapy.AssertionError()
path.append(oriented_segment)
def _initialize_positional_fields(self, strings):
if strings[0] != self.RECORD_TYPE and self.RECORD_TYPE != "\n":
raise gfapy.FormatError(
"Record type of records of " +
"class {} must be {} ({} found)".format(
self.__class__, self.RECORD_TYPE, strings[0]))
if self.version is None:
raise gfapy.AssertionError("Bug found, please report\n" +
"strings: {}".format(repr(strings)))
if (self.vlevel >= 1) and (len(strings) - 1 <
self._n_positional_fields):
raise gfapy.FormatError(
"{} positional fields expected, ".format(
self._n_positional_fields) +
"{} found\n{}".format(len(strings) - 1, repr(strings)))
for i, n in enumerate(self.POSFIELDS):
self._init_field_value(n,
self.__class__.DATATYPE[n],
strings[i + 1],
errmsginfo=strings)
def _unregister_line(self, gfa_line):
self._api_private_check_gfa_line(gfa_line, "unregister_line")
rt = gfa_line.record_type
if rt == "H":
raise gfapy.AssertionError("Bug found, please report\n" +
"gfa_line: {}".format(gfa_line))
collection = self._records[rt]
storage_key = gfa_line.__class__.STORAGE_KEY
if storage_key == "name":
name = gfa_line.name
if gfapy.is_placeholder(name):
name = id(gfa_line)
collection.pop(name)
elif storage_key == "external":
subkey = gfa_line.external.name
collection = collection[subkey]
collection.pop(id(gfa_line))
if not collection:
self._records[rt].pop(subkey)
else:
collection.pop(id(gfa_line))