biocantor.io.gff3.constants

Module Contents

Classes

GFF3Headers	Generic enumeration.
_GFF3ReservedQualifiers	These are special reserved qualifiers that BioCantor does not currently support.
BioCantorGFF3ReservedQualifiers	This is the subset of GFF3 reserved qualifiers that BioCantor currently reserves
BioCantorQualifiers	These are qualifiers that are added when exporting from BioCantor to GFF3, if they exist on the object.
GFF3GeneFeatureTypes	These are feature types seen in GFF3 files we are parsing that we currently understand.
BioCantorFeatureTypes	These are the feature types currently supported by BioCantor when writing genes, transcripts,

Attributes

ENCODING_MAP
ENCODING_MAP_WITH_COMMA
ENCODING_PATTERN
ENCODING_PATTERN_WITH_COMMA
GFF_SOURCE
NULL_COLUMN
ATTRIBUTE_SEPARATOR
GFF3ReservedQualifiers
BIOCANTOR_QUALIFIERS_REGEX

biocantor.io.gff3.constants.ENCODING_MAP

biocantor.io.gff3.constants.ENCODING_MAP_WITH_COMMA

biocantor.io.gff3.constants.ENCODING_PATTERN

biocantor.io.gff3.constants.ENCODING_PATTERN_WITH_COMMA

biocantor.io.gff3.constants.GFF_SOURCE = BioCantor

biocantor.io.gff3.constants.NULL_COLUMN = .

biocantor.io.gff3.constants.ATTRIBUTE_SEPARATOR = ,

class biocantor.io.gff3.constants.GFF3Headers

Bases: enum.Enum

Generic enumeration.

Derive from this class to define new enumerations.

HEADER = ##gff-version 3

FASTA_HEADER = ##FASTA

SEQUENCE_HEADER = ##sequence-region {symbol} 1 {length}

class biocantor.io.gff3.constants._GFF3ReservedQualifiers

Bases: inscripta.biocantor.util.enum.HasMemberMixin

These are special reserved qualifiers that BioCantor does not currently support.

All of these, if present in a qualifiers dictionary, will be simply included as-is.

See GFFAttributes for more information.

ALIAS = Alias

TARGET = Target

DBXREF = Dbxref

GAP = Gap

DERIVES_FROM = Derives_from

NOTE = Note

ONTOLOGY_TERM = Ontology_term

class biocantor.io.gff3.constants.BioCantorGFF3ReservedQualifiers

Bases: inscripta.biocantor.util.enum.HasMemberMixin

This is the subset of GFF3 reserved qualifiers that BioCantor currently reserves

NAME = Name

PARENT = Parent

ID = ID

biocantor.io.gff3.constants.GFF3ReservedQualifiers

class biocantor.io.gff3.constants.BioCantorQualifiers

Bases: enum.Enum

These are qualifiers that are added when exporting from BioCantor to GFF3, if they exist on the object.

Note that this enum does not filter arbitrary qualifier types, but rather exists to map attributes of an interval object on to the keys in the GFF3 attributes map.

TRANSCRIPT_ID = transcript_id

TRANSCRIPT_NAME = transcript_name

TRANSCRIPT_TYPE = transcript_biotype

PROTEIN_ID = protein_id

PRODUCT = product

GENE_ID = gene_id

GENE_SYMBOL = gene_name

GENE_NAME = gene_name

GENE_TYPE = gene_biotype

FEATURE_ID = feature_id

FEATURE_NAME = feature_name

FEATURE_SYMBOL = feature_name

FEATURE_COLLECTION_NAME = feature_collection_name

FEATURE_COLLECTION_ID = feature_collection_id

FEATURE_COLLETION_TYPE = feature_collection_type

FEATURE_TYPE = feature_type

LOCUS_TAG = locus_tag

biocantor.io.gff3.constants.BIOCANTOR_QUALIFIERS_REGEX

class biocantor.io.gff3.constants.GFF3GeneFeatureTypes

Bases: inscripta.biocantor.util.enum.HasMemberMixin

These are feature types seen in GFF3 files we are parsing that we currently understand.

GENE = gene

TRANSCRIPT = transcript

CDS = CDS

EXON = exon

PSEUDOGENE = pseudogene

class biocantor.io.gff3.constants.BioCantorFeatureTypes

Bases: inscripta.biocantor.util.enum.HasMemberMixin

These are the feature types currently supported by BioCantor when writing genes, transcripts, and feature collections to GFF3. When exporting features, the type of the feature is used directly.

TODO: Feature types should be explicitly linked to Sequence Ontology types. Biological region is a catch-all

term that matches both the INSDC specification as well as SO:0001411.

GENE = gene

TRANSCRIPT = transcript

CDS = CDS

EXON = exon

FEATURE_COLLECTION = biological_region

FEATURE_INTERVAL = feature_interval

FEATURE_INTERVAL_REGION = subregion