biocantor.io.genbank.constants
GenBank parsing constants. Records common feature types and their relationships as enumerations.
Module Contents
Classes
Currently implemented types of GenBank parsing. These types of files are not necessarily mutually exclusive, |
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GenBank metadata features BioCantor understands. |
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GenBank gene features BioCantor understands. |
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GenBank feature collections BioCantor understands. |
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GenBank transcript features types BioCantor understands. |
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Non-coding GenBank transcript features types BioCantor understands. |
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GenBank interval features types BioCantor understands. These do not match |
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GenBank interval features types BioCantor understands. These do not match |
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GenBank qualifiers that have special meaning |
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GenBank files are formatted differently at NCBI if the species is prokaryotic or eukaryotic. The main |
Attributes
- 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
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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