Bio2BEL FlyBase

A Bio2BEL package for FlyBase.

Manager for FlyBase.

class bio2bel_flybase.manager.Manager(*args, **kwargs)[source]

Manager for FlyBase.

count_fly_genes()[source]

Count the fly genes in the database.

Return type:int
is_populated()[source]

Check if the database is populated.

Return type:bool
namespace_model

alias of bio2bel_flybase.models.FlyGene

populate(gene_mapping_url=None)[source]

Populate the database.

summarize()[source]

Summarize the database.

Return type:Mapping[str, int]

FlyBase database models.

class bio2bel_flybase.models.FlyGene(**kwargs)[source]

Gene table.

serialize_to_protein_node()[source]

Serialize to PyBEL node data dictionary.

Return type:Gene

bio2bel_flybase

Default connection at sqlite:////home/docs/.bio2bel/bio2bel.db

using Bio2BEL v0.2.1

bio2bel_flybase [OPTIONS] COMMAND [ARGS]...

Options

-c, --connection <connection>

Defaults to sqlite:////home/docs/.bio2bel/bio2bel.db

belns

Manage BEL namespace.

bio2bel_flybase belns [OPTIONS] COMMAND [ARGS]...

drop

Clear names/identifiers to terminology store.

bio2bel_flybase belns drop [OPTIONS]

upload

Upload names/identifiers to terminology store.

bio2bel_flybase belns upload [OPTIONS]

Options

-u, --update

write

Write a BEL namespace names/identifiers to terminology store.

bio2bel_flybase belns write [OPTIONS]

Options

-f, --file <file>
-n, --use-names

cache

Manage cached data.

bio2bel_flybase cache [OPTIONS] COMMAND [ARGS]...

clear

Clear all files from the cache.

bio2bel_flybase cache clear [OPTIONS]

locate

Print the location of the data directory.

bio2bel_flybase cache locate [OPTIONS]

ls

List files in the cache.

bio2bel_flybase cache ls [OPTIONS]

drop

Drop the database.

bio2bel_flybase drop [OPTIONS]

Options

--yes

Confirm the action without prompting.

populate

Populate the database.

bio2bel_flybase populate [OPTIONS]

Options

--reset

Nuke database first

--force

Force overwrite if already populated

summarize

Summarize the contents of the database.

bio2bel_flybase summarize [OPTIONS]