Module 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.

Functions

_warn(message)

source code

_load_registry_objects(ini_file)

source code

_make_biofetch_db(name, tagvalue_dict)

source code

_make_biosql_db(name, tagvalue_dict)
Register a BioSQL database defined in the registry.

source code

_make_flat_db(name, tagvalue_dict)
Register a Berkeley or Flat indexed file defined in the registry.

source code

_openfu(file_or_url)
Guess whether this is a file or url and open it.

source code

list of URL's or paths to search for files

_list_ini_paths()
The default places to look for registry files are:

source code

list of files to search (in order)

_list_ini_files(filename)

source code

Variables

seqdb = seqdb

Function Details

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.