Module references

Documentation of the different modules and classes used in ncbi-taxonomist.

Contents

• Module references
  • ncbi-taxonomist
  • Analyzer
    • Accession analyzer: ncbitaxonomist.analyzer.accession
    • Collection analyzer: ncbitaxonomist.analyzer.collect
    • Mapping analyzer: ncbitaxonomist.analyzer.mapping
    • Resolve analyzer: ncbitaxonomist.analyzer.resolve
  • Cache
    • Cache module: ncbitaxonomist.cache
    • Taxa cache module: ncbitaxonomist.cache.taxa
    • Accession cache module: ncbitaxonomist.cache.accession
  • Converter
    • Base converter: ncbitaxonomist.convert.converter
    • Attribute mapping: ncbitaxonomist.convert.convertermap
    • Local database accession converter: ncbitaxonomist.convert.accessiondb
    • NCBI accessions converter: ncbitaxonomist.convert.ncbiaccession
    • NCBI taxon converter: ncbitaxonomist.convert.ncbitaxon
    • Local database taxon converter: ncbitaxonomist.convert.taxadb
  • Data models
    • Basic data model: ncbitaxonomist.model.datamodel
    • Taxon model: ncbitaxonomist.model.taxon
    • Accession Data model: ncbitaxonomist.model.accession
  • Database
    • Database manager: ncbitaxonomist.db.dbmanager
    • Database importer: ncbitaxonomist.db.dbimporter
    • Database tables
      • Base table: ncbitaxonomist.db.table.basetable
      • Taxa table: ncbitaxonomist.db.table.taxa
      • Names table: ncbitaxonomist.db.table.names
      • Accession table: ncbitaxonomist.db.table.accessions
      • Accession table: ncbitaxonomist.db.table.groups
  • Entrez results
    • Accession result: ncbitaxonomist.entrezresult.accession
    • Taxa cache module: ncbitaxonomist.entrezresult.mapping
    • Accession cache module: ncbitaxonomist.entrezresult.taxonomy
  • Formatter
    • Base module: ncbitaxonomist.formatter.base
    • JSON formatter: ncbitaxonomist.formatter.jsonformatter
    • XML formatter: ncbitaxonomist.formatter.xmlformatter
  • Logging
    • Configuration: ncbitaxonomist.log.conf
    • Logger: ncbitaxonomist.log.logger
  • Mappers
    • Mapper: ncbitaxonomist.mapper
    • Remote mapper: ncbitaxonomist.analyzer.mapping
    • Remote accession mapper: ncbitaxonomist.analyzer.accession
  • Parser
    • Argument parser: ncbitaxonomist.parser.arguments
    • Group data parser: ncbitaxonomist.parser.group
    • General stdout parser: ncbitaxonomist.parser.stdout
  • Queries
    • Collect queries
      • Base query: ncbitaxonomist.query.collect.collect
      • Name query: ncbitaxonomist.query.collect.name
      • Taxid query: ncbitaxonomist.query.collect.taxid
    • Map queries
      • Base query: ncbitaxonomist.query.map.map
      • Name query: ncbitaxonomist.query.map.name
      • Taxid query: ncbitaxonomist.query.map.taxid
      • Accession query: ncbitaxonomist.query.map.accession
    • Resolve queries
      • Base query: ncbitaxonomist.query.resolve.resolve
      • Name query: ncbitaxonomist.query.resolve.name
      • Taxid query: ncbitaxonomist.query.resolve.taxid
      • Accession query: ncbitaxonomist.query.resolve.accession
    • Remote query pipelines
  • Payloads
    • Base class for payloads: ncbitaxonomist.payload.payload
    • Taxid payload
    • Names payload
    • Accessions payload
    • Accession map payload
  • Resolver
  • Lineage resolver
  • Subtrees
    • Subtree
  • Subtree analyzer
  • Utility functions used across modules
    • Utility functions: ncbitaxonomist.utils

ncbi-taxonomist

This is the entry script for ncbi-taxonomist. It runs the requested command and checks its parameters.

Analyzer

Analyzer handle remote data from Entrez and are inherited from entrezpy.base.analyzer.EutilsAnalyzer.

Accession analyzer: ncbitaxonomist.analyzer.accession

Collection analyzer: ncbitaxonomist.analyzer.collect

Mapping analyzer: ncbitaxonomist.analyzer.mapping

Resolve analyzer: ncbitaxonomist.analyzer.resolve

Cache

Cache caches taxa to reuse already solved queries, avoiding unnessecary local or remote database lookups.

Cache module: ncbitaxonomist.cache

Taxa cache module: ncbitaxonomist.cache.taxa

Accession cache module: ncbitaxonomist.cache.accession

class ncbitaxonomist.cache.accession.AccessionCache

Class to handle caching of accessions. Accessions are stored mapping accessions as key and class:ncbitaxonomist.model.accession.AccessionData as value.

cache(acc: Type[ncbitaxonomist.model.accession.Accession])

Caches accession

get_accession(acc) → Type[ncbitaxonomist.model.accession.Accession]

Returns given or all taxids in cache

incache(name=None, taxid=None)

Tests if given accession is in cache.

is_empty()

Tests if cache is empty.

Converter

Converter convert between data models and pure attributes.

Base converter: ncbitaxonomist.convert.converter

class ncbitaxonomist.convert.converter.ModelConverter

Base class for converters between attributes and models.

convert_from_model(model: Type[ncbitaxonomist.model.datamodel.DataModel], outdict: Mapping[KT, VT_co] = None) → Dict[KT, VT]

Virtual method converts model to attributes

convert_to_model(attributes: Mapping[str, any], srcdb=None) → Type[ncbitaxonomist.model.datamodel.DataModel]

Virtual method converts attributes to model

map_inattributes(mattribs: Mapping[str, any], indata: Mapping[str, any], convmap: Mapping[str, str], switch: bool = False)

Map input attributes to wanted model attributes

Attribute mapping: ncbitaxonomist.convert.convertermap

Maps indicating which data attributes are convertred to which model attributes.

Local database accession converter: ncbitaxonomist.convert.accessiondb

class ncbitaxonomist.convert.accessiondb.DbAccessionConverter

Class implementing a converter for accession attributes and models

convert_from_model(model: Type[ncbitaxonomist.model.accession.Accession], outdict=None) → Dict[str, str]

Converts accession model to attributes

convert_to_model(attributes: Mapping[str, any], srcdb=None) → Type[ncbitaxonomist.model.accession.Accession]

Converts local database attributes to accession model

NCBI accessions converter: ncbitaxonomist.convert.ncbiaccession

class ncbitaxonomist.convert.ncbiaccession.NcbiAccessionConverter

Convert NCBI accession data into model or model into attributes

convert_from_model(model: Type[ncbitaxonomist.model.accession.Accession], outdict=None) → Dict[str, str]

Converts accession model to attributes

convert_to_model(attributes: Mapping[str, any], srcdb=None) → Type[ncbitaxonomist.model.accession.Accession]

Converts NCBI attributes to accession model

NCBI taxon converter: ncbitaxonomist.convert.ncbitaxon

Local database taxon converter: ncbitaxonomist.convert.taxadb

class ncbitaxonomist.convert.taxadb.TaxaDbConverter

Converts local database attributes into class:ncbitaxonomist.model.taxon.Taxon instances and vice versa

convert_from_model(model: Type[ncbitaxonomist.model.taxon.Taxon], outdict=None) → Dict[str, str]

Virtual method converts model to attributes

convert_to_model(attributes: Mapping, srcdb=None) → Type[ncbitaxonomist.model.taxon.Taxon]

Convert local database taxon attributes into class:ncbitaxonomist.model.taxon.Taxon

Data models

ncbi-taxonomist data models implement taxonomic and accession data. Models use a ncbitaxonomist.model.datamodel.DataModel as base class.

Basic data model: ncbitaxonomist.model.datamodel

class ncbitaxonomist.model.datamodel.DataModel(cast, attributes: Mapping[KT, VT_co] = None)

Base class for data models.

get_attributes() → Dict[str, any]

Return taxon attributes as dictionary.

classmethod new(attributes: Mapping[str, any] = None) → ncbitaxonomist.model.datamodel.DataModel

Return new instance with given attributes

classmethod new_from_json(json_attributes: str) → ncbitaxonomist.model.datamodel.DataModel

Return new instance with attributes encoded in JSON

taxid()

ncbitaxonomist.model.datamodel.int_attribute(attribute)

Enforce int for attribute

ncbitaxonomist.model.datamodel.standardize_attributes(attributes: Mapping[str, any])

Convert None into empty dictionary. See Important warning at https://docs.python.org/3/tutorial/controlflow.html#default-argument-values

Taxon model: ncbitaxonomist.model.taxon

Accession Data model: ncbitaxonomist.model.accession

class ncbitaxonomist.model.accession.Accession(attributes: Mapping[KT, VT_co] = None)

get_accessions() → Dict[str, str]

Return accessions as dictionary

get_attributes() → Dict[str, any]

Return taxon attributes as dictionary.

classmethod new(attributes: Mapping[str, any] = None) → ncbitaxonomist.model.datamodel.DataModel

Return new instance with given attributes

classmethod new_from_json(json_attributes: str) → ncbitaxonomist.model.datamodel.DataModel

Return new instance with attributes encoded in JSON

taxid()

update_accessions(accession: Mapping[str, str])

Update accessions from dictionary with structure accession:type

Database

Database modules for a local ncbi-taxonomist database

Database manager: ncbitaxonomist.db.dbmanager

Database importer: ncbitaxonomist.db.dbimporter

Database tables

Base table: ncbitaxonomist.db.table.basetable

class ncbitaxonomist.db.table.basetable.BaseTable(name: str, database: str)

Implements a basic table in a taxonomist database.

create(connection: Type[sqlite3.Connection]) → ncbitaxonomist.db.table.basetable.BaseTable

Virtual function to create table

create_index(connection: Type[sqlite3.Connection]) → None

Virtual function to create table index

insert(connection: Type[sqlite3.Connection], values: Tuple) → None

Virtual function to insert rows

Taxa table: ncbitaxonomist.db.table.taxa

class ncbitaxonomist.db.table.taxa.TaxaTable(database: str)

Implements taxa table for local taxonomy database.

create(connection: Type[sqlite3.Connection]) → ncbitaxonomist.db.table.taxa.TaxaTable

Virtual function to create table

create_index(connection: Type[sqlite3.Connection]) → None

Virtual function to create table index

get_lineage(connection: Type[sqlite3.Connection], taxid: int, name_table: str) → Type[sqlite3.Cursor]

Recursive construction of lineage from given taxid to highest parent.

get_rows(connection: Type[sqlite3.Connection]) → Type[sqlite3.Cursor]

get_subtree(connection: Type[sqlite3.Connection], taxid: int) → Type[sqlite3.Cursor]

Depth first search of taxon ids to find the subtree of taxid

get_taxids(connection: Type[sqlite3.Connection]) → Type[sqlite3.Cursor]

insert(connection: Type[sqlite3.Connection], taxavalues: Iterable[Tuple[int, str, int]]) → None

Virtual function to insert rows

insert_taxids(connection: Type[sqlite3.Connection], taxids: Iterable[int]) → None

Names table: ncbitaxonomist.db.table.names

class ncbitaxonomist.db.table.names.NameTable(database: str)

Implements the name table in a taxonomist database.

create(connection: Type[sqlite3.Connection]) → ncbitaxonomist.db.table.names.NameTable

Virtual function to create table

create_index(connection: Type[sqlite3.Connection])

Virtual function to create table index

get_rows(connection: Type[sqlite3.Connection]) → Type[sqlite3.Cursor]

insert(connection: Type[sqlite3.Connection], values: Tuple[int, str, str])

Virtual function to insert rows

name_to_taxid(connection: Type[sqlite3.Connection], name) → Type[sqlite3.Cursor]

Accession table: ncbitaxonomist.db.table.accessions

class ncbitaxonomist.db.table.accessions.AccessionTable(database)

create(connection: Type[sqlite3.Connection]) → ncbitaxonomist.db.table.accessions.AccessionTable

Virtual function to create table

create_index(connection: Type[sqlite3.Connection]) → None

Virtual function to create table index

get_rows(connection: Type[sqlite3.Connection]) → Type[sqlite3.Cursor]

insert(connection: Type[sqlite3.Connection], values: Iterable[Tuple[str, str, str, int, int]]) → None

Virtual function to insert rows

Accession table: ncbitaxonomist.db.table.groups

class ncbitaxonomist.db.table.groups.GroupTable(database: str)

create(connection: Type[sqlite3.Connection]) → ncbitaxonomist.db.table.groups.GroupTable

Virtual function to create table

create_index(connection: Type[sqlite3.Connection]) → None

Virtual function to create table index

delete_from_group(connection: Type[sqlite3.Connection], values: Iterable[Tuple[str, int]]) → None

delete_group(connection: Type[sqlite3.Connection], groupname: str) → None

insert(connection: Type[sqlite3.Connection], values: Iterable[Tuple[int, str]]) → None

Virtual function to insert rows

retrieve_group(connection: Type[sqlite3.Connection], groupname: str)

retrieve_names(connection: Type[sqlite3.Connection]) → Type[sqlite3.Cursor]

Entrez results

Implementations of Entrez results inherited from entrezpy.base.result.EutilsResult.

Accession result: ncbitaxonomist.entrezresult.accession

Taxa cache module: ncbitaxonomist.entrezresult.mapping

Accession cache module: ncbitaxonomist.entrezresult.taxonomy

Formatter

Formats JSON and XML outputs.

Base module: ncbitaxonomist.formatter.base

JSON formatter: ncbitaxonomist.formatter.jsonformatter

XML formatter: ncbitaxonomist.formatter.xmlformatter

Logging

Logging for ncbi-taxonomist.

Configuration: ncbitaxonomist.log.conf

Logger: ncbitaxonomist.log.logger

Mappers

Mappers handle the mapping of taxids, names, and accessions to each other. Analyzers are inherited and adjusted from entrezpy.

Mapper: ncbitaxonomist.mapper

Remote mapper: ncbitaxonomist.analyzer.mapping

Remote accession mapper: ncbitaxonomist.analyzer.accession

Parser

Parsers used in ncbi-taxonomist

Argument parser: ncbitaxonomist.parser.arguments

ncbitaxonomist.parser.arguments.parse(basename)

ncbitaxonomist.parser.arguments.version(basename)

Group data parser: ncbitaxonomist.parser.group

class ncbitaxonomist.parser.group.GroupParser

parse(groupname: str)

Parse stdin for taxonid to add into group groupname

parse_taxa_list(taxa_list, taxids, groupname)

parse_taxon(taxid, taxids, groupname)

General stdout parser: ncbitaxonomist.parser.stdout

Queries

Queries are modules implementing a specific taxonomic query, either remote or for a local database.

Collect queries

Queries to collect taxa remotely from Entrez.

Base query: ncbitaxonomist.query.collect.collect

Name query: ncbitaxonomist.query.collect.name

Taxid query: ncbitaxonomist.query.collect.taxid

Map queries

Queries to map taxa locally or remotely from Entrez.

Base query: ncbitaxonomist.query.map.map

Name query: ncbitaxonomist.query.map.name

Taxid query: ncbitaxonomist.query.map.taxid

Accession query: ncbitaxonomist.query.map.accession

Resolve queries

Queries to resolve taxa and accessions locally or remotely from Entrez.

Base query: ncbitaxonomist.query.resolve.resolve

Name query: ncbitaxonomist.query.resolve.name

Taxid query: ncbitaxonomist.query.resolve.taxid

Accession query: ncbitaxonomist.query.resolve.accession

Remote query pipelines

entrezpy.conduit pipelines to fetch remote query data.

Payloads

Payloads implement the requested taxids, names, and accessions. They keep track what has been successfully analyzed.

Base class for payloads: ncbitaxonomist.payload.payload

Taxid payload

Names payload

Accessions payload

Accession map payload

Resolver

The resolver module implements the resolving of lineages for names, taxids, and accessions.

Lineage resolver

The lineage resolver resolves whole lineages or the lienage taxa between given ranks.

Subtrees

Subtrees are selected taxa form lineages.

Subtree

Implemenets a subtree

Subtree analyzer

The subtree analyzer manages subtrees

Utility functions used across modules

Utility functions: ncbitaxonomist.utils