FTP (File Transfer Protocol) Documentation

The ftp module is geared towards making it easier to interface with NCBI’s FTP repository.

More specifically, we provide a way to easily find and list directories and their respective contents as well as to download blast databases and other databases for use with the Orthologs package. We have implemented database downloading with threading which is the safest way to implement this cross-platform.

We also provide a parallel module which can be used in conjunction with the NcbiFTPClient to download files or databases much quicker if your system can handle that.

If you’re using Linux or a supercomputer and do not want to use threading to download ftp databases, you can look at this cli script.

Examples

Blastdb Download Example

Download the latest blast databases (version 5 which is formatted for taxonomy ids). If v5=False, then the previously used blast databases will be downloaded. The taxdb.tar.gz database is also downloaded (by default) with the preformatted blast databases.

from OrthoEvol.Tools.ftp import NcbiFTPClient

ncbiftp = NcbiFTPClient(email='somebody@gmail.com')
ncbiftp.getblastdb(database_name='refseq_rna', v5=True)

Windowmasker files Download Example

from OrthoEvol.Tools.ftp import NcbiFTPClient
import os

ids = ['9544', '9606']

ncbiftp = NcbiFTPClient(email='somebody@gmail.com')
ncbiftp.getwindowmaskerfiles(taxonomy_ids=ids, download_path=os.getcwd())

Refseq Release Download Example

from OrthoEvol.Tools.ftp import NcbiFTPClient
import os

ncbiftp = NcbiFTPClient(email='somebody@gmail.com')
ncbiftp.getrefseqrelease(taxon_group='vertebrate_mammalian', seqtype='rna',
                         seqformat='gbff', download_path=os.getcwd())

List all directories in a path

ncbiftp.listdirectories(path='/blast/db/')
Out[54]: ['FASTA', 'cloud']

List all files in a path

ncbiftp.listfiles(path='/blast/db/')

List all files in the current working directory

# The default path is ftp.pwd() or the current directory
ncbiftp.listfiles()

Notes

Check the NCBI README for information about the preformatted blast databases that we use and suggest you use. We also provide an easy way to download them which is referenced in the above example.