def validate_decoded(obj):
if isinstance(obj, int):
pass
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name__) + "(accepted classes: str, int)")
def from_string(cls, string, valid=False):
"""
Create a numeric array from a string
Parameters
----------
string : str
valid : optional bool
*(default:* **False** *)*
If **False**, validate the range of the numeric values, according
to the array subtype. If **True** the string is guaranteed to be valid.
Raises
------
gfapy.ValueError
If any value is not compatible with the subtype.
gfapy.TypeError
If the subtype code is invalid.
Returns
-------
gfapy.NumericArray
The numeric array
"""
if not valid:
if len(string) == 0:
raise gfapy.FormatError(
"Numeric array string shall not be empty")
if string[-1] == ",":
raise gfapy.FormatError(
"Numeric array string ends with comma\n" +
"String: {}".format(string))
elems = string.split(",")
subtype = elems[0]
if subtype not in NumericArray.SUBTYPE:
raise gfapy.TypeError("Subtype {} unknown".format(subtype))
if subtype != "f":
range = NumericArray.SUBTYPE_RANGE[subtype]
def gen():
for e in elems[1:]:
if subtype != "f":
try:
e = int(e)
except:
raise gfapy.ValueError(
"Value is not valid: {}\n".format(e) +
"Numeric array string: {}".format(string))
if not valid and not (e >= range[0] and e < range[1]):
raise gfapy.ValueError(
("NumericArray: " +
"value is outside of subtype {0} range\n" +
"Value: {1}\n" + "Range: {2}\n" +
"Content: {3}").format(subtype, e, repr(range),
repr(elems)))
yield e
else:
yield float(e)
return cls(list(gen()))
def encode(obj):
if not isinstance(obj, str):
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name__) + "(accepted classes: str)")
validate_encoded(obj)
return obj
def validate(self, ts = None, version = "gfa2"):
"""Validates the trace alignment
Parameters:
ts (int): Trace Spacing. If specified, it will be checked that all values
are < **ts** (default: **None**, no check).
version (str) : GFA version (must be 'gfa1' or 'gfa2')
Raises:
~gfapy.error.TypeError: If the list contains non-integer values
~gfapy.error.ValueError: If the list contains values < 0 or > **ts**
~gfapy.error.VersionError: If the version is 'gfa1' or an invalid version
string is provided
"""
if version != "gfa2":
if version == "gfa1":
raise gfapy.VersionError("Traces are not compatible with GFA1")
else:
raise gfapy.VersionError("Version unknown: {}".format(repr(version)))
for e in self:
if not isinstance(e, int):
raise gfapy.TypeError(
("Trace contains non-integer values ({0} found)\n" + "Content: {1}")
.format(e, repr(self)))
if e < 0:
raise gfapy.ValueError(
("Trace contains value < 0 ({0} found)\n" + "Content: {1}")
.format(e, repr(self)))
if ts and e > ts:
raise gfapy.ValueError(
("Trace contains value > TS ({0} found, TS = {2})\n" + "Content: {1}")
.format(e, repr(self), ts))
def validate(self, version="gfa1"):
"""Validates the CIGAR operation.
Parameters:
version (str): 'gfa1' or 'gfa2'
Raises:
~gfapy.error.VersionError: If a wrong **version** is specified.
~gfapy.error.TypeError: If the CIGAR operation length is not an integer
or a string representing an integer.
~gfapy.error.ValueError: If the length of an operation is < 0; If an
operation code is invalid in general or for the specified GFA
version.
"""
if version != "gfa1" and version != "gfa2":
raise gfapy.VersionError("Version error: {}".format(
repr(version)))
if not isinstance(self.length, int) and not isinstance(
self.length, str):
raise gfapy.TypeError(
"Type error: length of CIGAR is {}".format(self.length))
if (int(self.length) < 0):
raise gfapy.ValueError("Length of CIGAR is {}".format(
self.length))
if version == "gfa2":
if not self.code in Operation.CODE_GFA1_GFA2:
raise gfapy.ValueError()
else:
if not self.code in Operation.CODE:
raise gfapy.ValueError()
def __validate_decoded_gfa_field(obj, datatype, fieldname=None):
"""Validate a non-string field content.
Parameters:
obj : the field content to validate
datatype (str) : the datatype identifier
fieldname (str) : for error messages
Raises:
gfapy.error.TypeError: if the specified datatype is invalid or the
object is of a class which is not compatible with the datatype
gfapy.error.FormatError: if the format of a string in the object
is not compatible with the datatype; or if the object encoded into
a GFA string is incompatible with the specification
gfapy.error.VersionError: if the object value is invalid
for the specific GFA version for which this datatype is used
gfapy.error.ValueError: if the value of the object is invalid
"""
if isinstance(obj, gfapy.FieldArray):
return obj._validate_gfa_field(datatype, fieldname=fieldname)
mod = gfapy.Field.FIELD_MODULE.get(datatype)
if not mod:
raise gfapy.TypeError("Datatype unknown: {}".format(
repr(datatype)))
return mod.validate_decoded(obj)
def unsafe_encode(obj):
if isinstance(obj, str):
return obj
elif isinstance(obj, list):
retval = []
for elem in obj:
if not isinstance(elem, gfapy.OrientedLine):
raise gfapy.TypeError(
"the list contains an object of class {}\n".format(type(elem))+
"(accepted classes: gfapy.OrientedLine)")
retval.append(str(elem))
return " ".join(retval)
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n"
.format(obj.__class__.__name__)+
"(accepted classes: str, list)")
def validate_decoded(obj):
if isinstance(obj, list):
for elem in obj:
if isinstance(elem, gfapy.Line):
elem = str(elem.name)
elif not isinstance(elem, str):
raise gfapy.TypeError("the list contains an obj of class {}\n".
format(elem.__class__.__name__) +
"(accepted classes: str, gfapy.Line)")
if not re.match("^[!-~]+$", elem):
raise gfapy.FormatError(
"the list contains an invalid GFA2 identifier ({})\n".
format(repr(string)) +
"(it contains spaces and/or non-printable characters)")
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name__) + "(accepted classes: list)")
def unsafe_encode(obj):
if isinstance(obj, str):
return obj
elif isinstance(obj, list):
return ",".join([str(gfapy.OrientedLine(os)) for os in obj])
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name__) + "(accepted classes: str, list)")
def func(elem):
if isinstance(elem, str):
return elem
elif isinstance(elem, gfapy.Line):
return str(elem.name)
else:
raise gfapy.TypeError("the list contains an obj of class {}\n".
format(elem.__class__.__name__) +
"(accepted classes: str, gfapy.Line)")
def __init__(self, verbose_level = 1, channel = sys.stderr, prefix = "#"):
self._progress = False
if not isinstance(verbose_level, int):
raise gfapy.ArgumentError("verbose_level must be an Integer")
if not(getattr(channel, "write", None) and callable(channel.write)):
raise gfapy.TypeError("channel must provide a 'write' method")
self._channel = channel
self._pfx = prefix
self._verbose_level = verbose_level
self._data = {}
def unsafe_encode(obj):
if isinstance(obj, gfapy.Placeholder):
return str(obj)
elif isinstance(obj, list):
return ",".join([str(gfapy.Alignment(cig)) for cig in obj])
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name__) +
"(accepted classes: list, AlignmentPlaceholder)")
def validate_decoded(obj):
if isinstance(obj, gfapy.CIGAR):
obj.validate()
elif isinstance(obj, gfapy.Placeholder):
pass
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name) +
"(accepted classes: gfapy.CIGAR, gfapy.Placeholder)")
def unsafe_encode(obj):
if isinstance(obj, str):
return obj
if isinstance(obj, gfapy.Line):
return str(obj.name)
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name__) +
"(accepted classes: str, gfapy.Line)")
def validate_decoded(obj):
if isinstance(obj, gfapy.Line):
validate_encoded(obj.name)
elif isinstance(obj, str):
validate_encoded(obj)
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name__) +
"(accepted classes: str, gfapy.Line)")
def _api_private_check_gfa_line(self, gfa_line, callermeth):
if not isinstance(gfa_line, gfapy.Line):
raise gfapy.TypeError("Note: {} is API private, ".format(callermeth)+
"do not call it directly\n"+
"Error: line class is {} and not gfapy.Line")
elif not gfa_line._gfa is self:
raise gfapy.RuntimeError("Note: {} is API private, ".format(callermeth)+
"do not call it directly\n"+
"Error: line.gfa is not the expected instance of gfapy.Gfa\n"+
repr(gfa_line.gfa)+" != "+repr(self))
def validate_decoded(obj):
if isinstance(obj, int):
if obj < 0:
raise gfapy.ValueError("{} is not a positive integer".format(obj))
elif isinstance(obj, gfapy.LastPos):
obj.validate()
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name__) +
"(accepted classes: int, gfapy.LastPos)")
def validate_decoded(obj):
if isinstance(obj, gfapy.FieldArray):
obj.validate()
elif isinstance(obj, list) or isinstance(obj, dict):
string = encode(obj)
validate_all_printable(string)
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name__) +
"(accepted classes: list, dict, gfapy.FieldArray)")
def encode(obj):
if isinstance(obj, str):
validate_encoded(obj)
return obj
elif isinstance(obj, int) or isinstance(obj, gfapy.Placeholder):
return str(obj)
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name__) +
"(accepted classes: int, str, gfapy.Placeholder)")
def validate_decoded(obj):
if isinstance(obj, gfapy.Placeholder):
pass
elif isinstance(obj, list):
for e in obj:
e = gfapy.Alignment(e, version="gfa1")
e.validate()
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name__) +
"(accepted classes: list, AlignmentPlaceholder)")
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 unsafe_encode(obj):
if isinstance(obj, gfapy.NumericArray):
return str(obj)
elif isinstance(obj, list):
return str(gfapy.NumericArray(obj))
elif isinstance(obj, str):
return obj
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name__) +
"(accepted classes: str, line, gfapy.NumericArray)")
def encode(obj):
if isinstance(obj, gfapy.ByteArray):
return str(obj)
elif isinstance(obj, list):
return str(ByteArray(obj))
elif isinstance(obj, str):
validate_encoded(obj)
return obj
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name__) +
"(accepted classes: str, list, gfapy.ByteArray)")
def __validate_line(self):
if isinstance(self.line, gfapy.Line):
string = self.line.name
elif isinstance(self.line, str):
string = self.line
else:
raise gfapy.TypeError(
"Invalid class ({}) for line reference ({})".format(
self.line.__class__, self.line))
if not re.match(r"^[!-~]+$", string):
raise gfapy.FormatError(
"{} is not a valid GFA identifier\n".format(repr(string)) +
"(it contains spaces or non-printable characters)")
def encode(obj):
if isinstance(obj, str):
validate_encoded(obj)
return obj
elif isinstance(obj, list) or isinstance(obj, dict):
string = json.dumps(obj)
validate_all_printable(string)
return string
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name__) +
"(accepted classes: list, dict, gfapy.FieldArray)")
def validate_decoded(obj):
if isinstance(obj, gfapy.OrientedLine):
if not re.match("^[!-~]+$", obj.name):
raise gfapy.FormatError(
"{} is not a valid oriented GFA2 identifier\n".format(repr(obj.name)))
if obj.orient != "+" and obj.orient != "-":
raise gfapy.FormatError(
"{} is not a valid orientation\n".format(repr(obj.orient)))
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n"
.format(obj.__class__.__name__)+
"(accepted classes: gfapy.OrientedLine)")
def encode(obj):
if isinstance(obj, gfapy.Placeholder):
return str(obj)
elif isinstance(obj, String):
obj = str(obj)
elif isinstance(obj, gfapy.Line):
obj = str(obj.name)
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name__) +
"(accepted classes: str, gfapy.Line, gfapy.Placeholder)")
validate_encoded(obj)
return obj
def induced_segments_set(self):
if not self.is_connected():
raise gfapy.RuntimeError(
"Induced set cannot be computed\n" +
"Line is not connected to a GFA instance\n" +
"Line: {}".format(self))
segments_set = list()
for item in self.items:
if isinstance(item, str):
raise gfapy.RuntimeError(
"Induced set cannot be computed; a reference has not been resolved\n"
+ "Line: {}\n".format(self) +
"Unresolved reference: {} (String found)".format(item.line)
)
elif isinstance(item, gfapy.line.segment.GFA2):
self._check_induced_set_elem_connected(item)
segments_set.append(item)
elif isinstance(item, gfapy.line.edge.GFA2):
self._check_induced_set_elem_connected(item)
for sl in [item.sid1.line, item.sid2.line]:
self._check_induced_set_elem_connected(sl)
segments_set.append(sl)
elif isinstance(item, gfapy.line.group.Ordered):
self._check_induced_set_elem_connected(item)
subset = item.captured_segments
assert (subset)
for elem in subset:
segments_set.append(elem.line)
elif isinstance(item, gfapy.line.group.Unordered):
self._check_induced_set_elem_connected(item)
subset = item.induced_segments_set
assert (subset)
for elem in subset:
segments_set.append(elem)
elif isinstance(item, gfapy.line.Unknown):
raise gfapy.RuntimeError(
"Induced set 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 induced set:\t" +
"Error: items of type {} are not supported\t".format(
item.__class__.__name__) +
"Unsupported item: {}".format(item))
unique_ids = set()
return [e for e in segments_set \
if id(e) not in unique_ids and not unique_ids.add(id(e))]
def encode(obj):
if isinstance(obj, str):
validate_encoded(obj)
return obj
elif isinstance(obj, gfapy.CIGAR) or isinstance(obj, gfapy.Trace):
obj.validate()
return str(obj)
elif isinstance(obj, gfapy.Placeholder):
return "*"
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name__) + "(accepted classes: " +
"str, CIGAR, Trace, AlignmentPlaceholder)")
def validate_decoded(iterable):
for elem in iterable:
if not isinstance(elem, gfapy.OrientedLine):
raise gfapy.TypeError(
"the list contains an object of class {}\n".format(type(elem))+
"(accepted classes: gfapy.OrientedLine)")
elem.validate()
if not re.match(r"^[!-~]+$", elem.name):
raise gfapy.FormatError(
"the list contains an invalid GFA2 identifier {}\n".format(elem.name)+
"(it contains spaces and/or non-printable characters)")
if not elem.orient in ["+", "-"]:
raise gfapy.FormatError(
"{} is not a valid orientation".format(elem.orient))