biocantor.io.genbank.constants

GenBank parsing constants. Records common feature types and their relationships as enumerations.

Module Contents

Classes

GenBankParserType	Currently implemented types of GenBank parsing. These types of files are not necessarily mutually exclusive,
MetadataFeatures	GenBank metadata features BioCantor understands.
GeneFeatures	GenBank gene features BioCantor understands.
FeatureCollectionFeatures	GenBank feature collections BioCantor understands.
TranscriptFeatures	GenBank transcript features types BioCantor understands.
NonCodingTranscriptFeatures	Non-coding GenBank transcript features types BioCantor understands.
GeneIntervalFeatures	GenBank interval features types BioCantor understands. These do not match
FeatureIntervalFeatures	GenBank interval features types BioCantor understands. These do not match
KnownQualifiers	GenBank qualifiers that have special meaning
GenbankFlavor	GenBank files are formatted differently at NCBI if the species is prokaryotic or eukaryotic. The main

Attributes

GENBANK_GENE_FEATURES

class biocantor.io.genbank.constants.GenBankParserType

Bases: enum.IntEnum

Currently implemented types of GenBank parsing. These types of files are not necessarily mutually exclusive, but the parsing implementations are different.

SORTED = 1

LOCUS_TAG = 2

HYBRID = 3

class biocantor.io.genbank.constants.MetadataFeatures

Bases: str, inscripta.biocantor.util.enum.HasMemberMixin

GenBank metadata features BioCantor understands.

SOURCE = 'source'

class biocantor.io.genbank.constants.GeneFeatures

Bases: str, inscripta.biocantor.util.enum.HasMemberMixin

GenBank gene features BioCantor understands.

GENE = 'gene'

class biocantor.io.genbank.constants.FeatureCollectionFeatures

Bases: str, inscripta.biocantor.util.enum.HasMemberMixin

GenBank feature collections BioCantor understands.

FEATURE_COLLECTION = 'misc_feature'

class biocantor.io.genbank.constants.TranscriptFeatures

Bases: str, inscripta.biocantor.util.enum.HasMemberMixin

GenBank transcript features types BioCantor understands.

CODING_TRANSCRIPT = 'mRNA'

NONCODING_TRANSCRIPT = 'ncRNA'

TRANSFER_RNA = 'tRNA'

RIBOSOMAL_RNA = 'rRNA'

MISC_RNA = 'misc_RNA'

TM_RNA = 'tmRNA'

class biocantor.io.genbank.constants.NonCodingTranscriptFeatures

Bases: str, inscripta.biocantor.util.enum.HasMemberMixin

Non-coding GenBank transcript features types BioCantor understands.

NONCODING_TRANSCRIPT = 'ncRNA'

TRANSFER_RNA = 'tRNA'

RIBOSOMAL_RNA = 'rRNA'

MISC_RNA = 'misc_RNA'

TM_RNA = 'tmRNA'

class biocantor.io.genbank.constants.GeneIntervalFeatures

Bases: str, inscripta.biocantor.util.enum.HasMemberMixin

GenBank interval features types BioCantor understands. These do not match

BioCantorFeatureTypes because GenBank has length limitations on feature types.

CDS = 'CDS'

EXON = 'exon'

class biocantor.io.genbank.constants.FeatureIntervalFeatures

Bases: str, inscripta.biocantor.util.enum.HasMemberMixin

GenBank interval features types BioCantor understands. These do not match

BioCantorFeatureTypes because GenBank has length limitations on feature types.

FEATURE_INTERVAL = 'feat_interval'

class biocantor.io.genbank.constants.KnownQualifiers

Bases: str, enum.Enum

GenBank qualifiers that have special meaning

GENE = 'gene'

LOCUS_TAG = 'locus_tag'

GENE_ID = 'gene_id'

TRANSCRIPT_ID = 'transcript_id'

PROTEIN_ID = 'protein_id'

PRODUCT = 'product'

GENE_NAME = 'gene_name'

GBKEY = 'gbkey'

DBXREF = 'db_xref'

GENE_SYNONYM = 'gene_synonym'

CODON_START = 'codon_start'

FEATURE_CLASS = 'feature_class'

biocantor.io.genbank.constants.GENBANK_GENE_FEATURES

class biocantor.io.genbank.constants.GenbankFlavor

Bases: enum.Enum

GenBank files are formatted differently at NCBI if the species is prokaryotic or eukaryotic. The main difference is the presence of a transcript level feature on eukaryotic genomes.

PROKARYOTIC = 1

EUKARYOTIC = 2