Manager.database_management.BaseDatabaseManagement

Usage

Source

Manager.database_management.BaseDatabaseManagement(
    email,
    driver,
    project=None,
    project_path=None,
    proj_mana=None,
    blast=False,
    ftp_flag=True
)

Methods

Name Description
__init__() This is the base class for managing various databases. It provides functionality for downloading and creating
copy_biosql_taxonomy_template() Copy a BioSQL template database loaded with NCBI’s taxonomy data.
create_biosql_taxonomy_template() Creates a template database by uploading SQLite schema and NCBI taxonomy.
download_blast_database() Download the blast database files for using NCBI’s BLAST+ command line.
download_ete3_taxonomy_database() Update ETE3’s taxonomy database with ETE3’s API.
download_ncbi_taxonomy_dump_files() Download and extract the NCBI taxonomy dump files via a GET request.
download_refseq_release_files() Download NCBI Refseq Release files from NCBI. The collection subtype is a species group
download_windowmasker_files() Download the WindowMasker files used in the BLAST database.
get_project_genbank_database()
upload_refseq_release_files() Upload NCBI’s Refseq Release files to a BioSQL database.

__init__()

This is the base class for managing various databases. It provides functionality for downloading and creating

Usage

Source

__init__(
    email,
    driver,
    project=None,
    project_path=None,
    proj_mana=None,
    blast=False,
    ftp_flag=True
)

various databases for your pipeline. There are functions available for downloading files from NCBI (BLAST, windowmasker, taxonomy, refseq release), downloading ITIS taxonomy tables, and creating BioSQL databases. This class currently REQUIRES an instance of ProjectManagement to be used with the proj_mana parameter.

Parameters
email: str

The email of the user for using during the FTP.

driver: str

The driver used for creating the BioSQL databases.

project: str | None = None

The name of the project.

project_path: str | Path | None = None

A path used for standalone/basic project configuration.

proj_mana: ProjectManagement | None = None

A configuration variable for connecting projects.

blast: bool = False

Flag for BLAST-related database operations.

ftp_flag: bool = True
A flag used if FTP connection is available or not.

copy_biosql_taxonomy_template()

Copy a BioSQL template database loaded with NCBI’s taxonomy data.

Usage

Source

copy_biosql_taxonomy_template(destination, database_name)
Parameters
destination: str.

Where the template will be copied to.

database_name: str.
The name of the copied database.

create_biosql_taxonomy_template()

Creates a template database by uploading SQLite schema and NCBI taxonomy.

Usage

Source

create_biosql_taxonomy_template()

download_blast_database()

Download the blast database files for using NCBI’s BLAST+ command line.

Usage

Source

download_blast_database(database_name="refseq_rna", v5=True, set_blastdb=True)

For other types of blast data, please see the NCBIREADME.md file.

Parameters
database_name: (str, optional) = "refseq_rna"

A string that represents a pattern in the files of interest, defaults to “refseq_rna”

v5: (bool, optional) = True

A flag that determines which version of blastdb to use, defaults to True

set_blastdb: (bool, optional) = True
A flag that determines whether the BLASTDB environment variable is automatically set.

download_ete3_taxonomy_database()

Update ETE3’s taxonomy database with ETE3’s API.

Usage

Source

download_ete3_taxonomy_database()

download_ncbi_taxonomy_dump_files()

Download and extract the NCBI taxonomy dump files via a GET request.

Usage

Source

download_ncbi_taxonomy_dump_files(
    url="ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz"
)
Parameters
url: str. = "ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz"
A ftp link to the NCBI taxdump*.tar.gz file of interest.

download_refseq_release_files()

Download NCBI Refseq Release files from NCBI. The collection subtype is a species group

Usage

Source

download_refseq_release_files(collection_subset, seqtype, seqformat)

(e.g. vertebrate_mammalian) of interest.

Parameters
collection_subset: str.

The collection subset of interest.

seqtype: str.

The type of sequence (RNA, protein, genomic).

seqformat: str.
The format of the sequence file (usually ‘gbff’ for GenBank Flat File).
Returns
list.
A list of files to download from NCBI via FTP.

download_windowmasker_files()

Download the WindowMasker files used in the BLAST database.

Usage

Source

download_windowmasker_files(taxonomy_ids)
Parameters
taxonomy_ids: list.
Taxonomy ids for the organisms of interest.

get_project_genbank_database()

Usage

Source

get_project_genbank_database()

upload_refseq_release_files()

Upload NCBI’s Refseq Release files to a BioSQL database.

Usage

Source

upload_refseq_release_files(
    collection_subset,
    seqtype,
    seqformat,
    upload_list=None,
    database_name=None,
    add_to_default=None
)
Parameters
collection_subset: str.

The collection subset of interest.

seqtype: str.

The type of sequence (RNA, protein, genomic).

seqformat: str.

The format of the sequence file (usually ‘gbff’ for GenBank Flat File).

upload_list: list. = None

A list of files to upload.

database_name: str. = None

The name of the database to create. The default name is usually best.

add_to_default: str. = None
A string to add to the default name.