Manager.biosql.biosql.BaseBioSQL

Usage

Source

Manager.biosql.biosql.BaseBioSQL(
    database_name,
    template_name="",
    project=None,
    project_path=None,
    proj_mana=ProjectManagement,
    **kwargs
)

Methods

Name Description
__init__() This is the base BioSQL class. It provides a general framework for managing the BioSQL workflow. Higher level
configure_new_database() This script is a framework for loading the various schemas, the NCBI taxonomy (biosql-db), and the ITIS
create_executable_scripts() Change permissions of the BioSQL perl scripts to make them executable.

__init__()

This is the base BioSQL class. It provides a general framework for managing the BioSQL workflow. Higher level

Usage

Source

__init__(
    database_name,
    template_name="",
    project=None,
    project_path=None,
    proj_mana=ProjectManagement,
    **kwargs
)

classes provide more specific functionality related to the various BioSQL supported database types. Taxonomy data can be found at: NCBI: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy ITIS: http://www.itis.gov/downloads/

Parameters
database_name: str.

The name of the database.

template_name: str. = ""

The name of the NCBI taxonomy database that will be copied for use.

project: str. = None

The name of the project, if Project Management isn’t utilized.

project_path: str. = None

Where the project is located if Project Management isn’t utilized.

proj_mana: ProjectManagement. = ProjectManagement

A configuration variable for connecting projects.

kwargs: dict. = {}
Key-word arguments.

configure_new_database()

This script is a framework for loading the various schemas, the NCBI taxonomy (biosql-db), and the ITIS

Usage

Source

configure_new_database(cmd, schema_file=None)

taxonomy (phylo-db) into a database.

Parameters
cmd: str.

The bash command to use.

schema_file: str. = None
The schema file for creating a BioSQL or PhyloDB
Returns
str.
Returns the Output and the Error messages.

create_executable_scripts()

Change permissions of the BioSQL perl scripts to make them executable.

Usage

Source

create_executable_scripts()