pyBlastDB is a tiny little program to automatically download complete directory trees from NCBI ftp server and generate a suitable blast database from the downloaded content. It is capable to generate nucleotide and protein blast databases from fasta content. Other file formats will not be provided at the moment.

Also pyBlastDB can generate an actual database for MetaCV, based on actual protein datasets on NCBI file server.

• python >= 2.7
• ncbi blast+ >= 2.2.27
• MetaCV >= 2.2.9

python pyBlastDB.py [-h] [--version] [-type {nucl,prot}] [-metacv] [-exe EXE]
                    -name NAME [-parse_seqids]

  -h, --help         show this help message and exit
  --version          show program's version number and exit
  -type {nucl,prot}  set type of blastdb
  -metacv            create metacv database
  -exe EXE           if not installed, specify path to executable of
                     'makeblastdb' or 'metacv'
  -name NAME         outname for the databases
  -parse_seqids      Remove duplicated GI numbers from downloaded files and
                     run "makeblastdb" with -parse_seqids statement

Download nucleotide datasets from NCBI ftp server and create a nucleotide blast database.

python pyBlastDB.py -type nucl -name bacterial -parse_seqids

Download protein datasets from NCBI ftp server and create a MetaCV database (without functional annotation).

python pyBlastDB.py -metacv -name bacterial

In the main script pyBlastDB.py following values can be adjusted to fit change the downloadable content. The variables for FTP sources can be customized for personal use. Over the sources list the selection for the database creation can be adjusted.

# FTP Sources
FTP_SERVER = 'ftp.ncbi.nih.gov' 
FTP_ROOT = 'genomes/'
BACTERIA = 'Bacteria'
BACTERIA_DRAFT = 'Bacteria_DRAFT'
PLASMIDS = 'Plasmids/'
VIRUSES = 'Viruses/'
FUNGI = 'Fungi/'
FUNGI_DRAFT = 'Fungi_DRAFT/'
HUMAN_BICROBIOM = 'HUMAN_MICROBIOM/Bacteria/'

# location for downloaded content
DOWNLOAD_FOLDER =  'sources'
# location of output db
DB_OUT = 'db_out'

# SELECT sources for database creation
SOURCES = [BACTERIA, BACTERIA_DRAFT, PLASMIDS, VIRUSES, FUNGI, FUNGI_DRAFT]