## Manager.biosql.biosql.BaseBioSQL


Usage

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


## Methods

| Name | Description |
|----|----|
| [__init__()](#__init__) | This is the base BioSQL class. It provides a general framework for managing the BioSQL workflow. Higher level |
| [configure_new_database()](#configure_new_database) | This script is a framework for loading the various schemas, the NCBI taxonomy (biosql-db), and the ITIS |
| [create_executable_scripts()](#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

``` python
__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

``` python
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

``` python
create_executable_scripts()
```