Term¶
Frame¶
AbstractEntityFrame
¶
- class fastobo.term.TermFrame(AbstractEntityFrame)¶
- __add__(value, /)¶
Return self+value.
- __delitem__(key, /)¶
Delete self[key].
- __getitem__(key, /)¶
Return self[key].
- __len__()¶
Return len(self).
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __setitem__(key, value, /)¶
Set self[key] to value.
- __str__()¶
Return str(self).
- append(object)¶
Append object to the end of the list.
- Raises:
TypeError – when the object is not of the right type for this container (see type-level documentation for the required type).
- clear()¶
Remove all items from list.
- copy()¶
Return a shallow copy of the list.
- count(value)¶
Return number of occurrences of value.
- Raises:
TypeError – when the object is not of the right type for this container (see type-level documentation for the required type).
- insert(index, object)¶
Insert
object
beforeindex
.If
index
is greater than the number of elements in the list,object
will be added at the end of the list.
- pop(index=-1)¶
Remove and return item at index (default last).
- Raises:
IndexError – when list is empty or index is out of range.
- reverse()¶
Reverse IN PLACE.
Clauses¶
BaseTermClause
¶
AltIdClause
¶
- class fastobo.term.AltIdClause(BaseTermClause)¶
AltIdClause(alt_id) –
A clause defines an alternate id for this term.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
BuiltinClause
¶
- class fastobo.term.BuiltinClause(BaseTermClause)¶
BuiltinClause(builtin) –
A clause declaring whether or not this term is built-in to the OBO format.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
CommentClause
¶
- class fastobo.term.CommentClause(BaseTermClause)¶
CommentClause(comment) –
A clause storing a comment for this term.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
ConsiderClause
¶
- class fastobo.term.ConsiderClause(BaseTermClause)¶
ConsiderClause(term) –
A clause giving a potential substitute for an obsolete term.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
CreatedByClause
¶
- class fastobo.term.CreatedByClause(BaseTermClause)¶
CreatedByClause(creator) –
A term clause stating the name of the creator of this term.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
CreationDateClause
¶
- class fastobo.term.CreationDateClause(BaseTermClause)¶
CreationDateClause(date) –
A clause declaring the date (and optionally time) a term was created.
- Parameters:
date (
datetime.date
) – The date this term was created. If adatetime.datime
object is given, then the serialized value will also include the serialized time.
Warning
The timezone of the
datetime
will only be extracted down to the minutes, seconds and smaller durations will be ignored. It is advised to usedatetime.timezone.utc
whenever possible to preserve the date and time properly.Example
>>> d1 = datetime.date(2021, 1, 23) >>> print(fastobo.term.CreationDateClause(d1)) creation_date: 2021-01-23 >>> d2 = datetime.datetime(2021, 1, 23, tzinfo=datetime.timezone.utc) >>> print(fastobo.term.CreationDateClause(d2)) creation_date: 2021-01-23T00:00:00Z
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- date¶
the date and time this term was created.
- Type:
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
DefClause
¶
- class fastobo.term.DefClause(BaseTermClause)¶
DefClause(definition, xrefs=None) –
A clause giving a human-readable definition of the term.
- Parameters:
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
- xrefs¶
a list of xrefs supporting the definition.
- Type:
XrefList
DisjointFromClause
¶
- class fastobo.term.DisjointFromClause(BaseTermClause)¶
DisjointFromClause(term) –
A clause stating this term has no instances in common with another term.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
EquivalentToClause
¶
- class fastobo.term.EquivalentToClause(BaseTermClause)¶
EquivalentToClause(term) –
A clause indicating the term is exactly equivalent to another term.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
- term¶
the identifier of the equivalent term.
- Type:
Ident
IntersectionOfClause
¶
- class fastobo.term.IntersectionOfClause(BaseTermClause)¶
IntersectionOfClause(typedef, term) –
A clause stating this term is equivalent to the intersection of other terms.
- Parameters:
typedef (Ident or None) – the identifier of the composing relationship, or
None
if the term is an intersection of other terms.term (Ident) – the identifier of the composing term.
Example
The following code describes the GO term
GO:0000085
(G2 phase of mitotic cell cycle) as being equivalent to any term which is both a subclass ofGO:0051319
(G2 phase) and has apart_of
relationship toGO:0000278
(mitotic cell cycle):>>> from fastobo.term import TermFrame, IntersectionOfClause >>> frame = TermFrame(fastobo.id.PrefixedIdent("GO", "0000085")) >>> frame.append(IntersectionOfClause( ... typedef=None, ... term=fastobo.id.PrefixedIdent("GO", "0051319")), ... ) >>> frame.append(IntersectionOfClause( ... typedef=fastobo.id.UnprefixedIdent("part_of"), ... term=fastobo.id.PrefixedIdent("GO", "0000278") ... ))
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
IsAClause
¶
- class fastobo.term.IsAClause(BaseTermClause)¶
IsAClause(term) –
A clause declaring this term is a subclass of another term.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
IsAnonymousClause
¶
- class fastobo.term.IsAnonymousClause(BaseTermClause)¶
IsAnonymousClause(anonymous) –
A clause declaring whether or not the current term has an anonymous id.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
IsObsoleteClause
¶
- class fastobo.term.IsObsoleteClause(BaseTermClause)¶
IsObsoleteClause(obsolete) –
A clause indicating whether or not this term is obsolete.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
NameClause
¶
- class fastobo.term.NameClause(BaseTermClause)¶
NameClause(name) –
A term clause declaring the human-readable name of this term.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
NamespaceClause
¶
- class fastobo.term.NamespaceClause(BaseTermClause)¶
NamespaceClause(namespace) –
A term clause declaring the namespace of this term.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
PropertyValueClause
¶
- class fastobo.term.PropertyValueClause(BaseTermClause)¶
PropertyValueClause(property_value) –
A clause that binds a property to a value in the term.
- Parameters:
property_value (AbstractPropertyValue) – the property value to annotate the current term.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- property_value¶
an annotation of the term.
- Type:
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
RelationshipClause
¶
- class fastobo.term.RelationshipClause(BaseTermClause)¶
RelationshipClause(typedef, term) –
A clause describing a typed relationship between this term and another term.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
ReplacedByClause
¶
- class fastobo.term.ReplacedByClause(BaseTermClause)¶
ReplacedByClause(term) –
A clause giving a term which replaces this obsolete term.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
SubsetClause
¶
- class fastobo.term.SubsetClause(BaseTermClause)¶
SubsetClause(subset) –
A clause declaring a subset to which this term belongs.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
SynonymClause
¶
- class fastobo.term.SynonymClause(BaseTermClause)¶
SynonymClause(synonym) –
A clause giving a synonym for this term, with some cross-references.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
UnionOfClause
¶
- class fastobo.term.UnionOfClause(BaseTermClause)¶
UnionOfClause(term) –
A clause indicating the term represents the union of several other terms.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'
- term¶
the identifier of the member term.
- Type:
Ident
XrefClause
¶
- class fastobo.term.XrefClause(BaseTermClause)¶
XrefClause(xref) –
A cross-reference that describes an analogous term in another vocabulary.
- __eq__(value, /)¶
Return self==value.
- __ge__(value, /)¶
Return self>=value.
- __gt__(value, /)¶
Return self>value.
- __hash__ = None¶
- __le__(value, /)¶
Return self<=value.
- __lt__(value, /)¶
Return self<value.
- __ne__(value, /)¶
Return self!=value.
- __new__(**kwargs)¶
- __repr__()¶
Return repr(self).
- __str__()¶
Return str(self).
- raw_tag()¶
Get the raw tag of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> clause = fastobo.header.OntologyClause("test") >>> clause.raw_tag() 'ontology' >>> str(clause) 'ontology: test'
- raw_value()¶
Get the raw value of the header clause.
- Returns:
str
– the header clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.
Example
>>> dt = datetime.datetime(2019, 4, 29, 21, 52) >>> clause = fastobo.header.DateClause(dt) >>> clause.date datetime.datetime(2019, 4, 29, 21, 52) >>> clause.raw_value() '29:04:2019 21:52'