biointerchange 0.2.0 → 0.2.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/README.md +11 -1
- data/VERSION +1 -1
- data/generators/javaify.rb +1 -1
- data/generators/rdfxml.rb +3 -1
- data/lib/biointerchange/core.rb +14 -13
- data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +61 -9
- data/lib/biointerchange/genomics/gff3_reader.rb +5 -1
- data/lib/biointerchange/gff3o.rb +44 -28
- data/lib/biointerchange/gvf1o.rb +63 -31
- data/lib/biointerchange/so.rb +19627 -0
- data/spec/gff3_rdfwriter_spec.rb +1 -1
- data/spec/gvf_rdfwriter_spec.rb +1 -1
- data/supplemental/java/biointerchange/pom.xml +1 -1
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java +97 -63
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java +686 -102
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SO.java +24000 -0
- data/supplemental/python/biointerchange/gff3o.py +85 -57
- data/supplemental/python/biointerchange/gvf1o.py +565 -84
- data/supplemental/python/biointerchange/so.py +19625 -0
- data/supplemental/python/setup.py +2 -2
- metadata +6 -3
@@ -9,6 +9,13 @@ def _namespace_GFF3O(accession):
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class GFF3O:
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@classmethod
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def seqid(cls):
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"""Establishes the landmark (cls, e.g. a chromosome) on which a feature is located.
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(GFF3_0004)
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"""
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return _namespace_GFF3O('GFF3_0004')
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@classmethod
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def strand(cls):
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"""Either:
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"""
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return [ _namespace_GFF3O('GFF3_0026'), _namespace_GFF3O('GFF3_0028') ]
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@classmethod
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def dbxref(cls):
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"""A database cross-reference to associate a sequence alteration to its representation in another database.
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(cls, GFF3_0034)
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"""
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return _namespace_GFF3O('GFF3_0034')
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@classmethod
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def ontology_term(cls):
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"""A cross-reference to an ontology term that is associated with a feature.
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(cls, GFF3_0035)
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"""
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return _namespace_GFF3O('GFF3_0035')
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@classmethod
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def target(cls):
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"""Identifies the target that the features aligns to.
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return _namespace_GFF3O('GFF3_0047')
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@classmethod
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def
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"""
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(cls,
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def feature_ontology(cls):
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"""Explicit link-out to one or more ontologies that have been used for describing features. This is a meta comment about the URIs that link out to SO/SOFA or other ontologies.
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(cls, GFF3_0056)
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"""
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return _namespace_GFF3O('
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return _namespace_GFF3O('GFF3_0056')
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@classmethod
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def source(cls):
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@classmethod
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def type(cls):
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"""Type of the feature, which is either
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"""Type of the feature, which is either an entry the "lite" version of the Sequence Ontology (cls, SOFA) or a child entry of sequence_feature (SO:0000110) of the full Sequence Ontology (SO).
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(GFF3_0006)
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"""
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return _namespace_GFF3O('GFF3_0006')
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Or:
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Start coordinate of the target.
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(GFF3_0042)
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Or:
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Genomic start coordinate of the landmark.
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(GFF3_0054)
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"""
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return [ _namespace_GFF3O('GFF3_0007'), _namespace_GFF3O('GFF3_0042') ]
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return [ _namespace_GFF3O('GFF3_0007'), _namespace_GFF3O('GFF3_0042'), _namespace_GFF3O('GFF3_0054') ]
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@classmethod
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def end(cls):
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Or:
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End coordinate of the target.
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(GFF3_0043)
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Or:
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Genomic end coordinate of the landmark.
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(GFF3_0055)
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"""
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return [ _namespace_GFF3O('GFF3_0008'), _namespace_GFF3O('GFF3_0043') ]
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return [ _namespace_GFF3O('GFF3_0008'), _namespace_GFF3O('GFF3_0043'), _namespace_GFF3O('GFF3_0055') ]
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@classmethod
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def score(cls):
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return _namespace_GFF3O('GFF3_0029')
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@classmethod
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def
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"""
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(cls,
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def dbxref(cls):
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"""A database cross-reference to associate a sequence alteration to its representation in another database.
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(cls, GFF3_0034)
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"""
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return _namespace_GFF3O('
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return _namespace_GFF3O('GFF3_0034')
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@classmethod
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def
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"""
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(cls, GFF3_0032)
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Or:
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Name of a feature, which can be used for display purposes. The name is not a unique property among features.
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(GFF3_0036)
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def ontology_term(cls):
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"""A cross-reference to an ontology term that is associated with a feature.
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(cls, GFF3_0035)
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"""
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return
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return _namespace_GFF3O('GFF3_0035')
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@classmethod
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def
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"""
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(cls,
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def name(cls):
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"""Name of a feature, which can be used for display purposes. The name is not a unique property among features.
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(cls, GFF3_0036)
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"""
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return _namespace_GFF3O('
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return _namespace_GFF3O('GFF3_0036')
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@classmethod
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def alias(cls):
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"""
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return _namespace_GFF3O('GFF3_0049')
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@classmethod
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def landmark_properties(cls):
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"""Properties that are directly associated with Landmark class instances.
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(cls, GFF3_0052)
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"""
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return _namespace_GFF3O('GFF3_0052')
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@classmethod
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def id(cls):
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"""ID that uniquely establishes the Landmark's identity within a Set.
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(cls, GFF3_0053)
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"""
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return _namespace_GFF3O('GFF3_0053')
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@classmethod
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def sequence(cls):
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"""Either:
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Sequence associated with this feature, if it has been specified using a FASTA string.
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(cls, GFF3_0057)
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Or:
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Sequence associated with this feature, if it has been specified using a FASTA string.
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(GFF3_0058)
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"""
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return [ _namespace_GFF3O('GFF3_0057'), _namespace_GFF3O('GFF3_0058') ]
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@classmethod
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def Set(cls):
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"""Set of genomic sequence features, whose identifiers are unique within the set.
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"""
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return _namespace_GFF3O('GFF3_0016')
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@classmethod
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def DBXRef(cls):
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"""A class describing relationships between features and external databases.
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(cls, GFF3_0030)
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"""
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return _namespace_GFF3O('GFF3_0030')
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@classmethod
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def Target(cls):
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"""Indicates a feature's "target" of a nucleotide-to-nucleotide or protein-to-nucleotide alignment.
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"""
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return _namespace_GFF3O('GFF3_0038')
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@classmethod
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def Landmark(cls):
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"""A landmark that establishes the coordinate system for features.
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(cls, GFF3_0051)
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"""
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return _namespace_GFF3O('GFF3_0051')
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@classmethod
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def Positive(cls):
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"""Location on the positive (cls, forward) strand.
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uri -- URI that is tested for being an object property
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"""
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if uri == _namespace_GFF3O('GFF3_0004'):
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return True
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if uri == _namespace_GFF3O('GFF3_0010'):
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return True
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if uri == _namespace_GFF3O('GFF3_0012'):
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return True
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if uri == _namespace_GFF3O('GFF3_0026'):
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return True
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if uri == _namespace_GFF3O('GFF3_0034'):
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return True
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return True
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return True
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return True
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if uri == _namespace_GFF3O('GFF3_0050'):
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return True
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if uri == _namespace_GFF3O('GFF3_0056'):
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return True
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return False
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@classmethod
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uri -- URI that is tested for being a datatype property
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"""
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return True
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if uri == _namespace_GFF3O('GFF3_0034'):
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return True
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if uri == _namespace_GFF3O('GFF3_0035'):
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return True
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return True
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return True
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if uri == _namespace_GFF3O('GFF3_0052'):
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return True
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return True
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if uri == _namespace_GFF3O('GFF3_0054'):
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return True
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if uri == _namespace_GFF3O('GFF3_0055'):
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return True
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return True
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return True
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@classmethod
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__parent_properties = { _namespace_GFF3O('
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__parent_properties = { _namespace_GFF3O('GFF3_0004') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0010') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0012') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0014') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0015') : _namespace_GFF3O('GFF3_0025') , _namespace_GFF3O('GFF3_0021') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0023') : _namespace_GFF3O('GFF3_0025') , _namespace_GFF3O('GFF3_0039') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0045') : _namespace_GFF3O('GFF3_0044') , _namespace_GFF3O('GFF3_0047') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0050') : _namespace_GFF3O('GFF3_0044') , _namespace_GFF3O('GFF3_0056') : _namespace_GFF3O('GFF3_0025') , _namespace_GFF3O('GFF3_0005') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0006') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0007') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0008') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0009') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0011') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0013') : _namespace_GFF3O('GFF3_0029') , _namespace_GFF3O('GFF3_0022') : _namespace_GFF3O('GFF3_0027') , _namespace_GFF3O('GFF3_0024') : _namespace_GFF3O('GFF3_0027') , _namespace_GFF3O('GFF3_0034') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0035') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0036') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0037') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0041') : _namespace_GFF3O('GFF3_0040') , _namespace_GFF3O('GFF3_0042') : _namespace_GFF3O('GFF3_0040') , _namespace_GFF3O('GFF3_0043') : _namespace_GFF3O('GFF3_0040') , _namespace_GFF3O('GFF3_0046') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0048') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0049') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0053') : _namespace_GFF3O('GFF3_0052') , _namespace_GFF3O('GFF3_0054') : _namespace_GFF3O('GFF3_0052') , _namespace_GFF3O('GFF3_0055') : _namespace_GFF3O('GFF3_0052') , _namespace_GFF3O('GFF3_0057') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0058') : _namespace_GFF3O('GFF3_0052') }
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class GVF1O:
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@classmethod
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def seqid(cls):
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"""Either:
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Establishes the landmark (cls, e.g. a chromosome) on which a feature is located.
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(GVF1_0004)
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Link to the landmark that establishes the coordinate system for the breakpoint.
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(GVF1_0072)
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"""
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def attributes(cls):
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Tag name/value pair attributes of a feature.
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(cls, GVF1_0012)
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Or:
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Tag name/value pair attributes that are not captured by the GVF specification.
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(GVF1_0152)
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"""
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return _namespace_GVF1O('GVF1_0012')
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return [ _namespace_GVF1O('GVF1_0012'), _namespace_GVF1O('GVF1_0152') ]
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def parent(cls):
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"""
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@classmethod
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def feature_id(cls):
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"""Features that are affected by this sequence alteration effect.
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(cls, GVF1_0044)
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"""
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return _namespace_GVF1O('GVF1_0044')
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def start_range(cls):
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"""
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"""Either:
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Properties that are directly associated with Effect class instances.
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(cls, GVF1_0070)
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Or:
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Properties that are directly associated with Effect class instances.
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(GVF1_0158)
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"""
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return [ _namespace_GVF1O('GVF1_0070'), _namespace_GVF1O('GVF1_0158') ]
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def breakpoint_properties(cls):
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def dbxref(cls):
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"""
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"""Either:
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A database cross-reference to associate a sequence alteration to its representation in another database.
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(cls, GVF1_0078)
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Or:
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A database cross-reference to associate a structured pragma to a representation in another database.
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(GVF1_0104)
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"""
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return [ _namespace_GVF1O('GVF1_0078'), _namespace_GVF1O('GVF1_0104') ]
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return [ _namespace_GVF1O('GVF1_0089'), _namespace_GVF1O('GVF1_0092') ]
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@classmethod
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def
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def technologyplatform_properties(cls):
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"""Either:
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-
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(cls,
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Properties that are directly associated with TechnologyPlatform class instances.
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(cls, GVF1_0102)
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Or:
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-
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(
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Properties that are directly associated with TechnologyPlatform class instances.
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(GVF1_0107)
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"""
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return [ _namespace_GVF1O('
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return [ _namespace_GVF1O('GVF1_0102'), _namespace_GVF1O('GVF1_0107') ]
|
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+
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@classmethod
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def datasource_properties(cls):
|
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"""Properties that are directly associated with DataSource class instances.
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(cls, GVF1_0103)
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"""
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return _namespace_GVF1O('GVF1_0103')
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@classmethod
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def structuredpragma_properties(cls):
|
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"""Either:
|
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Properties describing structured pragma properties.
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(cls, GVF1_0112)
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Or:
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Properties describing structured pragma properties.
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(GVF1_0113)
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"""
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return [ _namespace_GVF1O('GVF1_0112'), _namespace_GVF1O('GVF1_0113') ]
|
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+
|
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@classmethod
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def read_type(cls):
|
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"""Types of reads produced by the platform.
|
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(cls, GVF1_0119)
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+
"""
|
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return _namespace_GVF1O('GVF1_0119')
|
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+
|
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@classmethod
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def data_type(cls):
|
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"""Datatype of this data source.
|
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(cls, GVF1_0120)
|
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"""
|
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return _namespace_GVF1O('GVF1_0120')
|
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+
|
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+
@classmethod
|
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+
def technology_platform(cls):
|
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+
"""Technology platform that was used to derive the feature.
|
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(cls, GVF1_0121)
|
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+
"""
|
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return _namespace_GVF1O('GVF1_0121')
|
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+
|
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+
@classmethod
|
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def data_source(cls):
|
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"""Data source origin of the feature.
|
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(cls, GVF1_0122)
|
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+
"""
|
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return _namespace_GVF1O('GVF1_0122')
|
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+
|
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+
@classmethod
|
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|
+
def score_method(cls):
|
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"""Used scoring method.
|
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(cls, GVF1_0123)
|
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+
"""
|
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+
return _namespace_GVF1O('GVF1_0123')
|
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|
+
|
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|
+
@classmethod
|
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|
+
def source_method(cls):
|
314
|
+
"""Further information about the algorithm/methodologies used.
|
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|
+
(cls, GVF1_0124)
|
316
|
+
"""
|
317
|
+
return _namespace_GVF1O('GVF1_0124')
|
318
|
+
|
319
|
+
@classmethod
|
320
|
+
def phenotype_description(cls):
|
321
|
+
"""Further information about an individual's phenotype. Applies only to single individual sets.
|
322
|
+
(cls, GVF1_0125)
|
323
|
+
"""
|
324
|
+
return _namespace_GVF1O('GVF1_0125')
|
325
|
+
|
326
|
+
@classmethod
|
327
|
+
def attribute_method(cls):
|
328
|
+
"""Either:
|
329
|
+
Further information about the associated attribute(cls, s).
|
330
|
+
(GVF1_0126)
|
331
|
+
Or:
|
332
|
+
Further information about the associated attribute(s).
|
333
|
+
(GVF1_0127)
|
334
|
+
Or:
|
335
|
+
Further information about the associated attribute(s).
|
336
|
+
(GVF1_0129)
|
337
|
+
Or:
|
338
|
+
Further information about the associated attribute(s).
|
339
|
+
(GVF1_0130)
|
340
|
+
Or:
|
341
|
+
Further information about the associated attribute(s).
|
342
|
+
(GVF1_0131)
|
343
|
+
"""
|
344
|
+
return [ _namespace_GVF1O('GVF1_0126'), _namespace_GVF1O('GVF1_0127'), _namespace_GVF1O('GVF1_0129'), _namespace_GVF1O('GVF1_0130'), _namespace_GVF1O('GVF1_0131') ]
|
345
|
+
|
346
|
+
@classmethod
|
347
|
+
def attribute_properties(cls):
|
348
|
+
"""Either:
|
349
|
+
Properties about Attribute instances.
|
350
|
+
(cls, GVF1_0128)
|
351
|
+
Or:
|
352
|
+
Properties that are directly associated with Attribute class instances.
|
353
|
+
(GVF1_0064)
|
354
|
+
"""
|
355
|
+
return [ _namespace_GVF1O('GVF1_0128'), _namespace_GVF1O('GVF1_0064') ]
|
356
|
+
|
357
|
+
@classmethod
|
358
|
+
def sex(cls):
|
359
|
+
"""Denotes the sex of the sequenced individual for single-individual sets.
|
360
|
+
(cls, GVF1_0147)
|
361
|
+
"""
|
362
|
+
return _namespace_GVF1O('GVF1_0147')
|
363
|
+
|
364
|
+
@classmethod
|
365
|
+
def genomic_source(cls):
|
366
|
+
"""Denotes the source of genomic data (cls, on a cell-type level).
|
367
|
+
(GVF1_0148)
|
368
|
+
"""
|
369
|
+
return _namespace_GVF1O('GVF1_0148')
|
370
|
+
|
371
|
+
@classmethod
|
372
|
+
def feature_ontology(cls):
|
373
|
+
"""Explicit link-out to one or more ontologies that have been used for describing features. This is a meta comment about the URIs that link out to SO/SOFA or other ontologies.
|
374
|
+
(cls, GVF1_0150)
|
375
|
+
"""
|
376
|
+
return _namespace_GVF1O('GVF1_0150')
|
377
|
+
|
378
|
+
@classmethod
|
379
|
+
def target(cls):
|
380
|
+
"""Identifies the target that the features aligns to.
|
381
|
+
(cls, GVF1_0155)
|
382
|
+
"""
|
383
|
+
return _namespace_GVF1O('GVF1_0155')
|
242
384
|
|
243
385
|
@classmethod
|
244
386
|
def source(cls):
|
@@ -249,7 +391,7 @@ class GVF1O:
|
|
249
391
|
|
250
392
|
@classmethod
|
251
393
|
def type(cls):
|
252
|
-
"""Type of the feature, which is either
|
394
|
+
"""Type of the feature, which is either an entry the "lite" version of the Sequence Ontology (cls, SOFA) or a child entry of sequence_feature (SO:0000110) of the full Sequence Ontology (SO).
|
253
395
|
(GVF1_0006)
|
254
396
|
"""
|
255
397
|
return _namespace_GVF1O('GVF1_0006')
|
@@ -268,8 +410,11 @@ class GVF1O:
|
|
268
410
|
Or:
|
269
411
|
Start coordinate of the target.
|
270
412
|
(GVF1_0094)
|
413
|
+
Or:
|
414
|
+
Genomic start coordinate of the landmark.
|
415
|
+
(GVF1_0138)
|
271
416
|
"""
|
272
|
-
return [ _namespace_GVF1O('GVF1_0007'), _namespace_GVF1O('GVF1_0048'), _namespace_GVF1O('GVF1_0073'), _namespace_GVF1O('GVF1_0094') ]
|
417
|
+
return [ _namespace_GVF1O('GVF1_0007'), _namespace_GVF1O('GVF1_0048'), _namespace_GVF1O('GVF1_0073'), _namespace_GVF1O('GVF1_0094'), _namespace_GVF1O('GVF1_0138') ]
|
273
418
|
|
274
419
|
@classmethod
|
275
420
|
def end(cls):
|
@@ -285,8 +430,11 @@ class GVF1O:
|
|
285
430
|
Or:
|
286
431
|
End coordinate of the target.
|
287
432
|
(GVF1_0095)
|
433
|
+
Or:
|
434
|
+
Genomic end coordinate of the landmark.
|
435
|
+
(GVF1_0139)
|
288
436
|
"""
|
289
|
-
return [ _namespace_GVF1O('GVF1_0008'), _namespace_GVF1O('GVF1_0049'), _namespace_GVF1O('GVF1_0074'), _namespace_GVF1O('GVF1_0095') ]
|
437
|
+
return [ _namespace_GVF1O('GVF1_0008'), _namespace_GVF1O('GVF1_0049'), _namespace_GVF1O('GVF1_0074'), _namespace_GVF1O('GVF1_0095'), _namespace_GVF1O('GVF1_0139') ]
|
290
438
|
|
291
439
|
@classmethod
|
292
440
|
def score(cls):
|
@@ -297,10 +445,14 @@ class GVF1O:
|
|
297
445
|
|
298
446
|
@classmethod
|
299
447
|
def tag(cls):
|
300
|
-
"""
|
301
|
-
|
448
|
+
"""Either:
|
449
|
+
Tag name of a feature attribute.
|
450
|
+
(cls, GVF1_0013)
|
451
|
+
Or:
|
452
|
+
Tag name of an user defined structured attribute.
|
453
|
+
(GVF1_0154)
|
302
454
|
"""
|
303
|
-
return _namespace_GVF1O('GVF1_0013')
|
455
|
+
return [ _namespace_GVF1O('GVF1_0013'), _namespace_GVF1O('GVF1_0154') ]
|
304
456
|
|
305
457
|
@classmethod
|
306
458
|
def gvf_version(cls):
|
@@ -325,10 +477,14 @@ class GVF1O:
|
|
325
477
|
|
326
478
|
@classmethod
|
327
479
|
def id(cls):
|
328
|
-
"""
|
329
|
-
|
480
|
+
"""Either:
|
481
|
+
A unique identifier for the feature within the feature set.
|
482
|
+
(cls, GVF1_0026)
|
483
|
+
Or:
|
484
|
+
ID that uniquely establishes the Landmark's identity within a Set.
|
485
|
+
(GVF1_0137)
|
330
486
|
"""
|
331
|
-
return _namespace_GVF1O('GVF1_0026')
|
487
|
+
return [ _namespace_GVF1O('GVF1_0026'), _namespace_GVF1O('GVF1_0137') ]
|
332
488
|
|
333
489
|
@classmethod
|
334
490
|
def alias(cls):
|
@@ -337,20 +493,6 @@ class GVF1O:
|
|
337
493
|
"""
|
338
494
|
return _namespace_GVF1O('GVF1_0027')
|
339
495
|
|
340
|
-
@classmethod
|
341
|
-
def name(cls):
|
342
|
-
"""Name of an external database. For example, "dbSNP" or "OMIM".
|
343
|
-
(cls, GVF1_0029)
|
344
|
-
"""
|
345
|
-
return _namespace_GVF1O('GVF1_0029')
|
346
|
-
|
347
|
-
@classmethod
|
348
|
-
def xref(cls):
|
349
|
-
"""External database identifier. For example, for dbSNP, this identifier could be "rs3131969".
|
350
|
-
(cls, GVF1_0030)
|
351
|
-
"""
|
352
|
-
return _namespace_GVF1O('GVF1_0030')
|
353
|
-
|
354
496
|
@classmethod
|
355
497
|
def reference_seq(cls):
|
356
498
|
"""Sequence from the reference genome.
|
@@ -379,12 +521,23 @@ class GVF1O:
|
|
379
521
|
"""
|
380
522
|
return _namespace_GVF1O('GVF1_0039')
|
381
523
|
|
524
|
+
@classmethod
|
525
|
+
def feature(cls):
|
526
|
+
"""Features that are affected by this sequence alteration effect. This can be an external feature identifier, such as an Ensembl gene/transcript identifier.
|
527
|
+
(cls, GVF1_0044)
|
528
|
+
"""
|
529
|
+
return _namespace_GVF1O('GVF1_0044')
|
530
|
+
|
382
531
|
@classmethod
|
383
532
|
def phased(cls):
|
384
|
-
"""
|
385
|
-
|
533
|
+
"""Either:
|
534
|
+
Unclear from GVF specification.
|
535
|
+
(cls, GVF1_0050)
|
536
|
+
Or:
|
537
|
+
Indicates whether this particular is phased. Used to encode ##phased-genotypes statements.
|
538
|
+
(GVF1_0101)
|
386
539
|
"""
|
387
|
-
return _namespace_GVF1O('GVF1_0050')
|
540
|
+
return [ _namespace_GVF1O('GVF1_0050'), _namespace_GVF1O('GVF1_0101') ]
|
388
541
|
|
389
542
|
@classmethod
|
390
543
|
def variant_codon(cls):
|
@@ -421,20 +574,6 @@ class GVF1O:
|
|
421
574
|
"""
|
422
575
|
return _namespace_GVF1O('GVF1_0061')
|
423
576
|
|
424
|
-
@classmethod
|
425
|
-
def dbxref_properties(cls):
|
426
|
-
"""Properties that are directly associated with DBXRef class instances.
|
427
|
-
(cls, GVF1_0062)
|
428
|
-
"""
|
429
|
-
return _namespace_GVF1O('GVF1_0062')
|
430
|
-
|
431
|
-
@classmethod
|
432
|
-
def attribute_properties(cls):
|
433
|
-
"""Properties that are directly associated with Attribute class instances.
|
434
|
-
(cls, GVF1_0064)
|
435
|
-
"""
|
436
|
-
return _namespace_GVF1O('GVF1_0064')
|
437
|
-
|
438
577
|
@classmethod
|
439
578
|
def a_context(cls):
|
440
579
|
"""Sequence context (cls, positive strand) of a feature on the 5' end.
|
@@ -463,6 +602,87 @@ class GVF1O:
|
|
463
602
|
"""
|
464
603
|
return _namespace_GVF1O('GVF1_0093')
|
465
604
|
|
605
|
+
@classmethod
|
606
|
+
def ontology_term(cls):
|
607
|
+
"""A cross-reference to an ontology term that is associated with a feature.
|
608
|
+
(cls, GVF1_0096)
|
609
|
+
"""
|
610
|
+
return _namespace_GVF1O('GVF1_0096')
|
611
|
+
|
612
|
+
@classmethod
|
613
|
+
def comment(cls):
|
614
|
+
"""An arbitrary comment. Free text.
|
615
|
+
(cls, GVF1_0105)
|
616
|
+
"""
|
617
|
+
return _namespace_GVF1O('GVF1_0105')
|
618
|
+
|
619
|
+
@classmethod
|
620
|
+
def platform_class(cls):
|
621
|
+
"""Type of technology used to gather the variant data. Unrestricted range due to open specification.
|
622
|
+
(cls, GVF1_0106)
|
623
|
+
"""
|
624
|
+
return _namespace_GVF1O('GVF1_0106')
|
625
|
+
|
626
|
+
@classmethod
|
627
|
+
def platform_name(cls):
|
628
|
+
"""Sequencer or other machine used to collect the variant data. Unrestricted range due to open specification.
|
629
|
+
(cls, GVF1_0108)
|
630
|
+
"""
|
631
|
+
return _namespace_GVF1O('GVF1_0108')
|
632
|
+
|
633
|
+
@classmethod
|
634
|
+
def read_length(cls):
|
635
|
+
"""Undocumented in GVF specification.
|
636
|
+
(cls, GVF1_0132)
|
637
|
+
"""
|
638
|
+
return _namespace_GVF1O('GVF1_0132')
|
639
|
+
|
640
|
+
@classmethod
|
641
|
+
def read_pair_span(cls):
|
642
|
+
"""Undocumented in GVF specification.
|
643
|
+
(cls, GVF1_0133)
|
644
|
+
"""
|
645
|
+
return _namespace_GVF1O('GVF1_0133')
|
646
|
+
|
647
|
+
@classmethod
|
648
|
+
def average_coverage(cls):
|
649
|
+
"""Undocumented in GVF specification.
|
650
|
+
(cls, GVF1_0134)
|
651
|
+
"""
|
652
|
+
return _namespace_GVF1O('GVF1_0134')
|
653
|
+
|
654
|
+
@classmethod
|
655
|
+
def landmark_properties(cls):
|
656
|
+
"""Properties that are directly associated with Landmark class instances.
|
657
|
+
(cls, GVF1_0136)
|
658
|
+
"""
|
659
|
+
return _namespace_GVF1O('GVF1_0136')
|
660
|
+
|
661
|
+
@classmethod
|
662
|
+
def file_version(cls):
|
663
|
+
"""Version of the GVF file that this set stems from.
|
664
|
+
(cls, GVF1_0149)
|
665
|
+
"""
|
666
|
+
return _namespace_GVF1O('GVF1_0149')
|
667
|
+
|
668
|
+
@classmethod
|
669
|
+
def structuredattribute_properties(cls):
|
670
|
+
"""Properties that are directly associated with StructuredAttribute class instances.
|
671
|
+
(cls, GVF1_0153)
|
672
|
+
"""
|
673
|
+
return _namespace_GVF1O('GVF1_0153')
|
674
|
+
|
675
|
+
@classmethod
|
676
|
+
def sequence(cls):
|
677
|
+
"""Either:
|
678
|
+
Sequence associated with this feature, if it has been specified using a FASTA string.
|
679
|
+
(cls, GVF1_0156)
|
680
|
+
Or:
|
681
|
+
Sequence associated with this feature, if it has been specified using a FASTA string.
|
682
|
+
(GVF1_0157)
|
683
|
+
"""
|
684
|
+
return [ _namespace_GVF1O('GVF1_0156'), _namespace_GVF1O('GVF1_0157') ]
|
685
|
+
|
466
686
|
@classmethod
|
467
687
|
def Set(cls):
|
468
688
|
"""Set of genomic sequence features, whose identifiers are unique within the set.
|
@@ -479,6 +699,9 @@ class GVF1O:
|
|
479
699
|
|
480
700
|
@classmethod
|
481
701
|
def Attribute(cls):
|
702
|
+
"""Representation of attribute tag/value pairs that are not covered by specific classes such as Effect or Variant.
|
703
|
+
(cls, GVF1_0003)
|
704
|
+
"""
|
482
705
|
return _namespace_GVF1O('GVF1_0003')
|
483
706
|
|
484
707
|
@classmethod
|
@@ -488,13 +711,6 @@ class GVF1O:
|
|
488
711
|
"""
|
489
712
|
return _namespace_GVF1O('GVF1_0016')
|
490
713
|
|
491
|
-
@classmethod
|
492
|
-
def DBXRef(cls):
|
493
|
-
"""A class describing relationships between features and external databases.
|
494
|
-
(cls, GVF1_0028)
|
495
|
-
"""
|
496
|
-
return _namespace_GVF1O('GVF1_0028')
|
497
|
-
|
498
714
|
@classmethod
|
499
715
|
def Variant(cls):
|
500
716
|
"""Describing specific alterations of a feature.
|
@@ -551,6 +767,76 @@ class GVF1O:
|
|
551
767
|
"""
|
552
768
|
return _namespace_GVF1O('GVF1_0088')
|
553
769
|
|
770
|
+
@classmethod
|
771
|
+
def TechnologyPlatform(cls):
|
772
|
+
"""Details about the sequencing/microarray technology used to gather the data in a set.
|
773
|
+
(cls, GVF1_0097)
|
774
|
+
"""
|
775
|
+
return _namespace_GVF1O('GVF1_0097')
|
776
|
+
|
777
|
+
@classmethod
|
778
|
+
def DataSource(cls):
|
779
|
+
"""Provides information about the source of the data. For example, it can link out to actual sequences associated with the Feature individuals in a Set.
|
780
|
+
(cls, GVF1_0098)
|
781
|
+
"""
|
782
|
+
return _namespace_GVF1O('GVF1_0098')
|
783
|
+
|
784
|
+
@classmethod
|
785
|
+
def Method(cls):
|
786
|
+
"""Information about the used scoring algorithm or method.
|
787
|
+
(cls, GVF1_0099)
|
788
|
+
"""
|
789
|
+
return _namespace_GVF1O('GVF1_0099')
|
790
|
+
|
791
|
+
@classmethod
|
792
|
+
def PhenotypeDescription(cls):
|
793
|
+
"""Additional information about an individual's phenotype.
|
794
|
+
(cls, GVF1_0100)
|
795
|
+
"""
|
796
|
+
return _namespace_GVF1O('GVF1_0100')
|
797
|
+
|
798
|
+
@classmethod
|
799
|
+
def ReadType(cls):
|
800
|
+
"""Type of reads obtained for a given technology platform.
|
801
|
+
(cls, GVF1_0109)
|
802
|
+
"""
|
803
|
+
return _namespace_GVF1O('GVF1_0109')
|
804
|
+
|
805
|
+
@classmethod
|
806
|
+
def DataType(cls):
|
807
|
+
"""Determines the datatype of a variant sequence.
|
808
|
+
(cls, GVF1_0114)
|
809
|
+
"""
|
810
|
+
return _namespace_GVF1O('GVF1_0114')
|
811
|
+
|
812
|
+
@classmethod
|
813
|
+
def Landmark(cls):
|
814
|
+
"""A landmark that establishes the coordinate system for features.
|
815
|
+
(cls, GVF1_0135)
|
816
|
+
"""
|
817
|
+
return _namespace_GVF1O('GVF1_0135')
|
818
|
+
|
819
|
+
@classmethod
|
820
|
+
def Sex(cls):
|
821
|
+
"""For single individual sets, the Sex class' OWL-individuals can be used to specify the sex of the sequenced (cls, real-life) individuals.
|
822
|
+
(GVF1_0140)
|
823
|
+
"""
|
824
|
+
return _namespace_GVF1O('GVF1_0140')
|
825
|
+
|
826
|
+
@classmethod
|
827
|
+
def GenomicSource(cls):
|
828
|
+
"""An enumerated class for determining the genomic source (cls, cell type) of sequenced data.
|
829
|
+
(GVF1_0141)
|
830
|
+
"""
|
831
|
+
return _namespace_GVF1O('GVF1_0141')
|
832
|
+
|
833
|
+
@classmethod
|
834
|
+
def StructuredAttribute(cls):
|
835
|
+
"""Representation of attribute tag/value pairs that are specific to particular structured attributes, but which are not covered by the GVF specification.
|
836
|
+
(cls, GVF1_0151)
|
837
|
+
"""
|
838
|
+
return _namespace_GVF1O('GVF1_0151')
|
839
|
+
|
554
840
|
@classmethod
|
555
841
|
def Positive(cls):
|
556
842
|
"""Location on the positive (cls, forward) strand.
|
@@ -600,12 +886,91 @@ class GVF1O:
|
|
600
886
|
"""
|
601
887
|
return _namespace_GVF1O('GVF1_0087')
|
602
888
|
|
889
|
+
@classmethod
|
890
|
+
def Fragment(cls):
|
891
|
+
"""Denotes reads that are fragments.
|
892
|
+
(cls, GVF1_0110)
|
893
|
+
"""
|
894
|
+
return _namespace_GVF1O('GVF1_0110')
|
895
|
+
|
896
|
+
@classmethod
|
897
|
+
def Pair(cls):
|
898
|
+
"""Denotes reads that are pairs.
|
899
|
+
(cls, GVF1_0111)
|
900
|
+
"""
|
901
|
+
return _namespace_GVF1O('GVF1_0111')
|
902
|
+
|
903
|
+
@classmethod
|
904
|
+
def DNASequence(cls):
|
905
|
+
"""Denotes a DNA sequence.
|
906
|
+
(cls, GVF1_0115)
|
907
|
+
"""
|
908
|
+
return _namespace_GVF1O('GVF1_0115')
|
909
|
+
|
910
|
+
@classmethod
|
911
|
+
def RNASequence(cls):
|
912
|
+
"""Denotes an RNA sequence.
|
913
|
+
(cls, GVF1_0116)
|
914
|
+
"""
|
915
|
+
return _namespace_GVF1O('GVF1_0116')
|
916
|
+
|
917
|
+
@classmethod
|
918
|
+
def DNAMicroarray(cls):
|
919
|
+
"""Denotes a DNA microarray probe.
|
920
|
+
(cls, GVF1_0117)
|
921
|
+
"""
|
922
|
+
return _namespace_GVF1O('GVF1_0117')
|
923
|
+
|
924
|
+
@classmethod
|
925
|
+
def ArrayComparativeGenomicHybridization(cls):
|
926
|
+
"""Denotes an array-comparative genomic hybridization.
|
927
|
+
(cls, GVF1_0118)
|
928
|
+
"""
|
929
|
+
return _namespace_GVF1O('GVF1_0118')
|
930
|
+
|
931
|
+
@classmethod
|
932
|
+
def Female(cls):
|
933
|
+
"""Denotes that a Set contains features of a female.
|
934
|
+
(cls, GVF1_0142)
|
935
|
+
"""
|
936
|
+
return _namespace_GVF1O('GVF1_0142')
|
937
|
+
|
938
|
+
@classmethod
|
939
|
+
def Male(cls):
|
940
|
+
"""Denotes that a Set contains features of a male.
|
941
|
+
(cls, GVF1_0143)
|
942
|
+
"""
|
943
|
+
return _namespace_GVF1O('GVF1_0143')
|
944
|
+
|
945
|
+
@classmethod
|
946
|
+
def Prenatal(cls):
|
947
|
+
"""Denotes that a set contains features of prenatal cells.
|
948
|
+
(cls, GVF1_0144)
|
949
|
+
"""
|
950
|
+
return _namespace_GVF1O('GVF1_0144')
|
951
|
+
|
952
|
+
@classmethod
|
953
|
+
def Germline(cls):
|
954
|
+
"""Denotes that a set contains features of germline cells.
|
955
|
+
(cls, GVF1_0145)
|
956
|
+
"""
|
957
|
+
return _namespace_GVF1O('GVF1_0145')
|
958
|
+
|
959
|
+
@classmethod
|
960
|
+
def Somatic(cls):
|
961
|
+
"""Denotes that a set contains features of somatic cells.
|
962
|
+
(cls, GVF1_0146)
|
963
|
+
"""
|
964
|
+
return _namespace_GVF1O('GVF1_0146')
|
965
|
+
|
603
966
|
@classmethod
|
604
967
|
def is_object_property(cls, uri):
|
605
968
|
"""Determines whether the given URI is an object property.
|
606
969
|
|
607
970
|
uri -- URI that is tested for being an object property
|
608
971
|
"""
|
972
|
+
if uri == _namespace_GVF1O('GVF1_0004'):
|
973
|
+
return True
|
609
974
|
if uri == _namespace_GVF1O('GVF1_0010'):
|
610
975
|
return True
|
611
976
|
if uri == _namespace_GVF1O('GVF1_0012'):
|
@@ -630,8 +995,6 @@ class GVF1O:
|
|
630
995
|
return True
|
631
996
|
if uri == _namespace_GVF1O('GVF1_0043'):
|
632
997
|
return True
|
633
|
-
if uri == _namespace_GVF1O('GVF1_0044'):
|
634
|
-
return True
|
635
998
|
if uri == _namespace_GVF1O('GVF1_0046'):
|
636
999
|
return True
|
637
1000
|
if uri == _namespace_GVF1O('GVF1_0047'):
|
@@ -650,6 +1013,8 @@ class GVF1O:
|
|
650
1013
|
return True
|
651
1014
|
if uri == _namespace_GVF1O('GVF1_0070'):
|
652
1015
|
return True
|
1016
|
+
if uri == _namespace_GVF1O('GVF1_0072'):
|
1017
|
+
return True
|
653
1018
|
if uri == _namespace_GVF1O('GVF1_0075'):
|
654
1019
|
return True
|
655
1020
|
if uri == _namespace_GVF1O('GVF1_0078'):
|
@@ -666,6 +1031,50 @@ class GVF1O:
|
|
666
1031
|
return True
|
667
1032
|
if uri == _namespace_GVF1O('GVF1_0091'):
|
668
1033
|
return True
|
1034
|
+
if uri == _namespace_GVF1O('GVF1_0102'):
|
1035
|
+
return True
|
1036
|
+
if uri == _namespace_GVF1O('GVF1_0103'):
|
1037
|
+
return True
|
1038
|
+
if uri == _namespace_GVF1O('GVF1_0104'):
|
1039
|
+
return True
|
1040
|
+
if uri == _namespace_GVF1O('GVF1_0112'):
|
1041
|
+
return True
|
1042
|
+
if uri == _namespace_GVF1O('GVF1_0119'):
|
1043
|
+
return True
|
1044
|
+
if uri == _namespace_GVF1O('GVF1_0120'):
|
1045
|
+
return True
|
1046
|
+
if uri == _namespace_GVF1O('GVF1_0121'):
|
1047
|
+
return True
|
1048
|
+
if uri == _namespace_GVF1O('GVF1_0122'):
|
1049
|
+
return True
|
1050
|
+
if uri == _namespace_GVF1O('GVF1_0123'):
|
1051
|
+
return True
|
1052
|
+
if uri == _namespace_GVF1O('GVF1_0124'):
|
1053
|
+
return True
|
1054
|
+
if uri == _namespace_GVF1O('GVF1_0125'):
|
1055
|
+
return True
|
1056
|
+
if uri == _namespace_GVF1O('GVF1_0126'):
|
1057
|
+
return True
|
1058
|
+
if uri == _namespace_GVF1O('GVF1_0127'):
|
1059
|
+
return True
|
1060
|
+
if uri == _namespace_GVF1O('GVF1_0128'):
|
1061
|
+
return True
|
1062
|
+
if uri == _namespace_GVF1O('GVF1_0129'):
|
1063
|
+
return True
|
1064
|
+
if uri == _namespace_GVF1O('GVF1_0130'):
|
1065
|
+
return True
|
1066
|
+
if uri == _namespace_GVF1O('GVF1_0131'):
|
1067
|
+
return True
|
1068
|
+
if uri == _namespace_GVF1O('GVF1_0147'):
|
1069
|
+
return True
|
1070
|
+
if uri == _namespace_GVF1O('GVF1_0148'):
|
1071
|
+
return True
|
1072
|
+
if uri == _namespace_GVF1O('GVF1_0150'):
|
1073
|
+
return True
|
1074
|
+
if uri == _namespace_GVF1O('GVF1_0152'):
|
1075
|
+
return True
|
1076
|
+
if uri == _namespace_GVF1O('GVF1_0155'):
|
1077
|
+
return True
|
669
1078
|
return False
|
670
1079
|
|
671
1080
|
@classmethod
|
@@ -674,8 +1083,6 @@ class GVF1O:
|
|
674
1083
|
|
675
1084
|
uri -- URI that is tested for being a datatype property
|
676
1085
|
"""
|
677
|
-
if uri == _namespace_GVF1O('GVF1_0004'):
|
678
|
-
return True
|
679
1086
|
if uri == _namespace_GVF1O('GVF1_0005'):
|
680
1087
|
return True
|
681
1088
|
if uri == _namespace_GVF1O('GVF1_0006'):
|
@@ -698,10 +1105,6 @@ class GVF1O:
|
|
698
1105
|
return True
|
699
1106
|
if uri == _namespace_GVF1O('GVF1_0027'):
|
700
1107
|
return True
|
701
|
-
if uri == _namespace_GVF1O('GVF1_0029'):
|
702
|
-
return True
|
703
|
-
if uri == _namespace_GVF1O('GVF1_0030'):
|
704
|
-
return True
|
705
1108
|
if uri == _namespace_GVF1O('GVF1_0031'):
|
706
1109
|
return True
|
707
1110
|
if uri == _namespace_GVF1O('GVF1_0032'):
|
@@ -710,6 +1113,8 @@ class GVF1O:
|
|
710
1113
|
return True
|
711
1114
|
if uri == _namespace_GVF1O('GVF1_0039'):
|
712
1115
|
return True
|
1116
|
+
if uri == _namespace_GVF1O('GVF1_0044'):
|
1117
|
+
return True
|
713
1118
|
if uri == _namespace_GVF1O('GVF1_0048'):
|
714
1119
|
return True
|
715
1120
|
if uri == _namespace_GVF1O('GVF1_0049'):
|
@@ -730,8 +1135,6 @@ class GVF1O:
|
|
730
1135
|
return True
|
731
1136
|
if uri == _namespace_GVF1O('GVF1_0061'):
|
732
1137
|
return True
|
733
|
-
if uri == _namespace_GVF1O('GVF1_0062'):
|
734
|
-
return True
|
735
1138
|
if uri == _namespace_GVF1O('GVF1_0063'):
|
736
1139
|
return True
|
737
1140
|
if uri == _namespace_GVF1O('GVF1_0064'):
|
@@ -740,8 +1143,6 @@ class GVF1O:
|
|
740
1143
|
return True
|
741
1144
|
if uri == _namespace_GVF1O('GVF1_0071'):
|
742
1145
|
return True
|
743
|
-
if uri == _namespace_GVF1O('GVF1_0072'):
|
744
|
-
return True
|
745
1146
|
if uri == _namespace_GVF1O('GVF1_0073'):
|
746
1147
|
return True
|
747
1148
|
if uri == _namespace_GVF1O('GVF1_0074'):
|
@@ -762,6 +1163,46 @@ class GVF1O:
|
|
762
1163
|
return True
|
763
1164
|
if uri == _namespace_GVF1O('GVF1_0095'):
|
764
1165
|
return True
|
1166
|
+
if uri == _namespace_GVF1O('GVF1_0096'):
|
1167
|
+
return True
|
1168
|
+
if uri == _namespace_GVF1O('GVF1_0101'):
|
1169
|
+
return True
|
1170
|
+
if uri == _namespace_GVF1O('GVF1_0105'):
|
1171
|
+
return True
|
1172
|
+
if uri == _namespace_GVF1O('GVF1_0106'):
|
1173
|
+
return True
|
1174
|
+
if uri == _namespace_GVF1O('GVF1_0107'):
|
1175
|
+
return True
|
1176
|
+
if uri == _namespace_GVF1O('GVF1_0108'):
|
1177
|
+
return True
|
1178
|
+
if uri == _namespace_GVF1O('GVF1_0113'):
|
1179
|
+
return True
|
1180
|
+
if uri == _namespace_GVF1O('GVF1_0132'):
|
1181
|
+
return True
|
1182
|
+
if uri == _namespace_GVF1O('GVF1_0133'):
|
1183
|
+
return True
|
1184
|
+
if uri == _namespace_GVF1O('GVF1_0134'):
|
1185
|
+
return True
|
1186
|
+
if uri == _namespace_GVF1O('GVF1_0136'):
|
1187
|
+
return True
|
1188
|
+
if uri == _namespace_GVF1O('GVF1_0137'):
|
1189
|
+
return True
|
1190
|
+
if uri == _namespace_GVF1O('GVF1_0138'):
|
1191
|
+
return True
|
1192
|
+
if uri == _namespace_GVF1O('GVF1_0139'):
|
1193
|
+
return True
|
1194
|
+
if uri == _namespace_GVF1O('GVF1_0149'):
|
1195
|
+
return True
|
1196
|
+
if uri == _namespace_GVF1O('GVF1_0153'):
|
1197
|
+
return True
|
1198
|
+
if uri == _namespace_GVF1O('GVF1_0154'):
|
1199
|
+
return True
|
1200
|
+
if uri == _namespace_GVF1O('GVF1_0156'):
|
1201
|
+
return True
|
1202
|
+
if uri == _namespace_GVF1O('GVF1_0157'):
|
1203
|
+
return True
|
1204
|
+
if uri == _namespace_GVF1O('GVF1_0158'):
|
1205
|
+
return True
|
765
1206
|
return False
|
766
1207
|
|
767
1208
|
@classmethod
|
@@ -778,8 +1219,6 @@ class GVF1O:
|
|
778
1219
|
return True
|
779
1220
|
if uri == _namespace_GVF1O('GVF1_0016'):
|
780
1221
|
return True
|
781
|
-
if uri == _namespace_GVF1O('GVF1_0028'):
|
782
|
-
return True
|
783
1222
|
if uri == _namespace_GVF1O('GVF1_0033'):
|
784
1223
|
return True
|
785
1224
|
if uri == _namespace_GVF1O('GVF1_0035'):
|
@@ -796,6 +1235,26 @@ class GVF1O:
|
|
796
1235
|
return True
|
797
1236
|
if uri == _namespace_GVF1O('GVF1_0088'):
|
798
1237
|
return True
|
1238
|
+
if uri == _namespace_GVF1O('GVF1_0097'):
|
1239
|
+
return True
|
1240
|
+
if uri == _namespace_GVF1O('GVF1_0098'):
|
1241
|
+
return True
|
1242
|
+
if uri == _namespace_GVF1O('GVF1_0099'):
|
1243
|
+
return True
|
1244
|
+
if uri == _namespace_GVF1O('GVF1_0100'):
|
1245
|
+
return True
|
1246
|
+
if uri == _namespace_GVF1O('GVF1_0109'):
|
1247
|
+
return True
|
1248
|
+
if uri == _namespace_GVF1O('GVF1_0114'):
|
1249
|
+
return True
|
1250
|
+
if uri == _namespace_GVF1O('GVF1_0135'):
|
1251
|
+
return True
|
1252
|
+
if uri == _namespace_GVF1O('GVF1_0140'):
|
1253
|
+
return True
|
1254
|
+
if uri == _namespace_GVF1O('GVF1_0141'):
|
1255
|
+
return True
|
1256
|
+
if uri == _namespace_GVF1O('GVF1_0151'):
|
1257
|
+
return True
|
799
1258
|
return False
|
800
1259
|
|
801
1260
|
@classmethod
|
@@ -818,6 +1277,28 @@ class GVF1O:
|
|
818
1277
|
return True
|
819
1278
|
if uri == _namespace_GVF1O('GVF1_0087'):
|
820
1279
|
return True
|
1280
|
+
if uri == _namespace_GVF1O('GVF1_0110'):
|
1281
|
+
return True
|
1282
|
+
if uri == _namespace_GVF1O('GVF1_0111'):
|
1283
|
+
return True
|
1284
|
+
if uri == _namespace_GVF1O('GVF1_0115'):
|
1285
|
+
return True
|
1286
|
+
if uri == _namespace_GVF1O('GVF1_0116'):
|
1287
|
+
return True
|
1288
|
+
if uri == _namespace_GVF1O('GVF1_0117'):
|
1289
|
+
return True
|
1290
|
+
if uri == _namespace_GVF1O('GVF1_0118'):
|
1291
|
+
return True
|
1292
|
+
if uri == _namespace_GVF1O('GVF1_0142'):
|
1293
|
+
return True
|
1294
|
+
if uri == _namespace_GVF1O('GVF1_0143'):
|
1295
|
+
return True
|
1296
|
+
if uri == _namespace_GVF1O('GVF1_0144'):
|
1297
|
+
return True
|
1298
|
+
if uri == _namespace_GVF1O('GVF1_0145'):
|
1299
|
+
return True
|
1300
|
+
if uri == _namespace_GVF1O('GVF1_0146'):
|
1301
|
+
return True
|
821
1302
|
return False
|
822
1303
|
|
823
1304
|
@classmethod
|
@@ -842,5 +1323,5 @@ class GVF1O:
|
|
842
1323
|
return cls.has_parent(cls.__parent_properties[uri], parent)
|
843
1324
|
return False
|
844
1325
|
|
845
|
-
__parent_properties = { _namespace_GVF1O('GVF1_0010') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0012') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0014') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0015') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0021') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0023') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0034') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0036') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0038') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0041') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0042') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0043') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('
|
1326
|
+
__parent_properties = { _namespace_GVF1O('GVF1_0004') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0010') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0012') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0014') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0015') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0021') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0023') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0034') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0036') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0038') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0041') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0042') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0043') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0046') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0047') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0051') : _namespace_GVF1O('GVF1_0067') , _namespace_GVF1O('GVF1_0053') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0072') : _namespace_GVF1O('GVF1_0075') , _namespace_GVF1O('GVF1_0078') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0079') : _namespace_GVF1O('GVF1_0075') , _namespace_GVF1O('GVF1_0080') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0083') : _namespace_GVF1O('GVF1_0075') , _namespace_GVF1O('GVF1_0090') : _namespace_GVF1O('GVF1_0089') , _namespace_GVF1O('GVF1_0091') : _namespace_GVF1O('GVF1_0089') , _namespace_GVF1O('GVF1_0102') : _namespace_GVF1O('GVF1_0112') , _namespace_GVF1O('GVF1_0103') : _namespace_GVF1O('GVF1_0112') , _namespace_GVF1O('GVF1_0104') : _namespace_GVF1O('GVF1_0112') , _namespace_GVF1O('GVF1_0119') : _namespace_GVF1O('GVF1_0102') , _namespace_GVF1O('GVF1_0120') : _namespace_GVF1O('GVF1_0103') , _namespace_GVF1O('GVF1_0121') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0122') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0123') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0124') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0125') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0126') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0127') : _namespace_GVF1O('GVF1_0075') , _namespace_GVF1O('GVF1_0129') : _namespace_GVF1O('GVF1_0128') , _namespace_GVF1O('GVF1_0130') : _namespace_GVF1O('GVF1_0089') , _namespace_GVF1O('GVF1_0131') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0147') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0148') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0150') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0152') : _namespace_GVF1O('GVF1_0112') , _namespace_GVF1O('GVF1_0155') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0005') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0006') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0007') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0008') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0009') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0013') : _namespace_GVF1O('GVF1_0064') , _namespace_GVF1O('GVF1_0022') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0024') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0025') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0026') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0027') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0031') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0032') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0037') : _namespace_GVF1O('GVF1_0065') , _namespace_GVF1O('GVF1_0039') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0044') : _namespace_GVF1O('GVF1_0158') , _namespace_GVF1O('GVF1_0048') : _namespace_GVF1O('GVF1_0061') , _namespace_GVF1O('GVF1_0049') : _namespace_GVF1O('GVF1_0061') , _namespace_GVF1O('GVF1_0050') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0054') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0055') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0056') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0057') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0073') : _namespace_GVF1O('GVF1_0071') , _namespace_GVF1O('GVF1_0074') : _namespace_GVF1O('GVF1_0071') , _namespace_GVF1O('GVF1_0076') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0077') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0081') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0082') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0093') : _namespace_GVF1O('GVF1_0092') , _namespace_GVF1O('GVF1_0094') : _namespace_GVF1O('GVF1_0092') , _namespace_GVF1O('GVF1_0095') : _namespace_GVF1O('GVF1_0092') , _namespace_GVF1O('GVF1_0096') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0101') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0105') : _namespace_GVF1O('GVF1_0113') , _namespace_GVF1O('GVF1_0106') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0107') : _namespace_GVF1O('GVF1_0113') , _namespace_GVF1O('GVF1_0108') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0132') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0133') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0134') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0137') : _namespace_GVF1O('GVF1_0136') , _namespace_GVF1O('GVF1_0138') : _namespace_GVF1O('GVF1_0136') , _namespace_GVF1O('GVF1_0139') : _namespace_GVF1O('GVF1_0136') , _namespace_GVF1O('GVF1_0149') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0154') : _namespace_GVF1O('GVF1_0153') , _namespace_GVF1O('GVF1_0156') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0157') : _namespace_GVF1O('GVF1_0136') , _namespace_GVF1O('GVF1_0088') : _namespace_GVF1O('http://www.w3.org/2002/07/owl#Thing') , _namespace_GVF1O('GVF1_0151') : _namespace_GVF1O('http://www.w3.org/2002/07/owl#Thing') }
|
846
1327
|
|