Bio.config.SeqDBRegistry

Package Bio :: Package config :: Module SeqDBRegistry

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Module Bio.config.SeqDBRegistry

This module handles seqdatabase.INI file.

Classes: SeqDBRegistry Holds databases from seqdatabase.INI.

Classes
`SeqDBRegistry`	This object implements a dictionary-like interface to sequence databases.

Function Summary
	`_list_ini_files(filename, also_search)` _list_ini_files(filename) -> list of files to search (in order)
	`_list_ini_paths()` _list_ini_paths() -> list of URL's or paths to search for files.
	`_load_registry_objects(ini_file)`
	`_make_biofetch_db(name, tagvalue_dict)`
	`_make_biosql_db(name, tagvalue_dict)` Register a BioSQL database defined in the registry.
	`_make_flat_db(name, tagvalue_dict)` Register a Berkeley or Flat indexed file defined in the registry.
	`_openfu(file_or_url)` Guess whether this is a file or url and open it.
	`_warn(message)`

Function Details

_list_ini_files(filename, also_search=[])

_list_ini_files(filename) -> list of files to search (in order)

_list_ini_paths()

_list_ini_paths() -> list of URL's or paths to search for files.

The default places to look for registry files are:
- ${HOME}/.bioinformatics
- /etc/bioinformatics
- http://www.open-bio.org/registry

The OBDA_SEARCH_PATH environment variable, if specified, overrides
the default.  This should be a "+" separated list of paths or
URL's.

_make_biosql_db(name, tagvalue_dict)

_make_flat_db(name, tagvalue_dict)

_openfu(file_or_url)

Guess whether this is a file or url and open it.

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