Tools.ftp.NcbiFTPClient

Access NCBI directories over FTP and download data over HTTPS.

Usage

Source

Tools.ftp.NcbiFTPClient(
    email,
    max_workers=4,
    **kwargs,
)

Methods

Name Description
__init__() Initialize an anonymous NCBI connection.
download_file() Download a file from the current or specified NCBI directory.
extract_file() Extract a gzip or tar-gzip archive into a controlled directory.
getblastdb() Download a complete preformatted NCBI BLAST database.
getblastfasta() Download one of NCBI’s convenience BLAST FASTA archives.
getrefseqrelease() Download one molecule and format selection from a RefSeq release.
getwindowmaskerfiles() Reject downloads from NCBI’s retired WindowMasker file service.
listdirectories() List subdirectories in an FTP directory.
listfiles() List files in an FTP directory.
updatedb() Refresh recognized local databases after a minimum age.
walk() List immediate directories and files in an NCBI FTP path.

__init__()

Initialize an anonymous NCBI connection.

Usage

Source

__init__(email, max_workers=4, **kwargs)
Parameters
email: str

Contact email used as the anonymous FTP password.

max_workers: int = 4

Maximum number of concurrent HTTPS transfers.

kwargs: Any = {}
Additional arguments for BaseFTPClient.

download_file()

Download a file from the current or specified NCBI directory.

Usage

Source

download_file(filename, download_path=".")
Parameters
filename: str

Remote file name or absolute remote path.

download_path: str | Path = "."
Local destination directory.
Returns
Path
Local file path.

extract_file()

Extract a gzip or tar-gzip archive into a controlled directory.

Usage

Source

extract_file(file2extract, download_path=None, remove_archive=True)

getblastdb()

Download a complete preformatted NCBI BLAST database.

Usage

Source

getblastdb(
    database_name, download_path, v5=True, extract=True, include_taxonomy=True
)

Version 5 selections come from NCBI’s metadata manifest, which avoids partial or substring-based database matches.

getblastfasta()

Download one of NCBI’s convenience BLAST FASTA archives.

Usage

Source

getblastfasta(database_name, download_path, extract=True)

getrefseqrelease()

Download one molecule and format selection from a RefSeq release.

Usage

Source

getrefseqrelease(
    collection_subset, seqtype, seqformat, download_path, extract=True
)

getwindowmaskerfiles()

Reject downloads from NCBI’s retired WindowMasker file service.

Usage

Source

getwindowmaskerfiles(taxonomy_ids, download_path)

listdirectories()

List subdirectories in an FTP directory.

Usage

Source

listdirectories(path="cwd")
Parameters
path: str = "cwd"
Absolute directory path or cwd.
Returns
list[str]
Sorted directory names.

listfiles()

List files in an FTP directory.

Usage

Source

listfiles(path="cwd")
Parameters
path: str = "cwd"
Absolute directory path or cwd.
Returns
list[str]
Sorted file names.

updatedb()

Refresh recognized local databases after a minimum age.

Usage

Source

updatedb(database_path=None, update_days=7)

walk()

List immediate directories and files in an NCBI FTP path.

Usage

Source

walk(path)
Parameters
path: str
Absolute FTP directory path.
Returns
tuple[list[str], list[str]]
Directory names followed by file names.