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)

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.

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