Taxonize_genbank is a python package useful to download, filter, and curated the Genbank non-redundant protein and nucleotide databases, based on a given taxonomy ID (TaxID) and/or list of keywords.
To use this tool, make sure you have the following libraries installed:
- Python 3.7 or higher
- Biopython: 1.81
- tqdm: 4.64.1
- ete3: 3.1.3
- networkx: 2.6.3
- six: 1.16.0
Please make sure to install these dependencies before using the tool.
Then, you can clone this repository to your local machine using git.
Open your terminal and run the following command:
git clone https://github.com/msabrysarhan/taxonize_genbankOr alternatively (recomended), you can install taxonize_gb using using pip:
pip install taxonize-gbTaxonize_gb has three main modules:
- get_db.py
usage: get_db.py [-h] --db_name DB_NAME --out OUT
Download NCBI databases.
optional arguments:
-h, --help show this help message and exit
--db_name DB_NAME Which NCBI database to be downloaded.
Possible values are the following:
'taxdb': The NCBI taxonomy dump database files.
'nr': The non-redundant protein database.
'nt': The non-redundant nucleotide database.
'prot_acc2taxid': GenBank protein accession number to taxonomy ID mapping file.
'pdb_acc2taxid': Protein Database (PDB) accession number to taxonomy ID mapping file.
'nucl_gb_acc2taxid': Nucleotide (GenBank, GB) accession number to taxonomy ID mapping file.
'nucl_wgs_acc2taxid': Nucleotide (Whole Genome Shotgun, WGS) accession number to taxonomy ID mapping file.
--out OUT Path to output directory where the results are to be stored.- taxonize_gb.py
usage: taxonize_gb.py [-h] --db DB [--db_path DB_PATH] [--taxdb TAXDB]
[--prot_acc2taxid PROT_ACC2TAXID]
[--pdb_acc2taxid PDB_ACC2TAXID]
[--nucl_gb_acc2taxid NUCL_GB_ACC2TAXID]
[--nucl_wgs_acc2taxid NUCL_WGS_ACC2TAXID]
[--taxid TAXID] [--keywords KEYWORDS] --out OUT
Filter NCBI nt/nr database based on a given taxid.
optional arguments:
-h, --help show this help message and exit
--db DB Which NCBI database to be used. Please use either nt
for nucleotide database or nr for protein database
--db_path DB_PATH Path to nt/nr gzipped fasta file (if not provided, the
latest version will be downloaded from the NCBI (must
be provided with --db)
--taxdb TAXDB Path to gzipped taxonomy database from the NCBI (if
not provided, the latest version will be downloaded
from the NCBI
--prot_acc2taxid PROT_ACC2TAXID
Path to gzipped GenBank protein accession number to
taxid mapping file from the NCBI; works with --db nr
(if not provided, the latest version will be
downloaded from the NCBI
--pdb_acc2taxid PDB_ACC2TAXID
Path to gzipped PDB protein accession number to taxid
mapping file from the NCBI; works with --db nr (if not
provided, the latest version will be downloaded from
the NCBI
--nucl_gb_acc2taxid NUCL_GB_ACC2TAXID
Path to gzipped Genbank nucleotide accession number to
taxid mapping file from the NCBI; works with --db nt
(if not provided, the latest version will be
downloaded from the NCBI
--nucl_wgs_acc2taxid NUCL_WGS_ACC2TAXID
Path to gzipped whole genome sequence accession number
to taxid mapping file from the NCBI; works with --db
nt (if not provided, the latest version will be
downloaded from the NCBI
--taxid TAXID Target taxonomy ID to filter for
--keywords KEYWORDS keywords to be included in the fasta headers of the
target taxonomy ID
--out OUT Path to output directory where the results are to be
stored.- get_taxonomy.py
usage: get_taxonomy.py [-h] --fasta FASTA --map MAP --out OUT
Get taxonomic lineages of FASTA accessions.
optional arguments:
-h, --help show this help message and exit
--fasta FASTA NCBI FASTA file to be filtered.
--map MAP Accession number to taxonomy IDs gzipped mapping file.
--out OUT Path to output file to write the taxonomic lineages of the GenBank accession numbers.- Plant non-redundant protein database
First, we need to use the get_db module to download the following files to a directory databases:
# The nr FASTA file
get_db --db_name nr --out databases
# The NCBI accession to taxonomy ID mapping file
get_db --db_name prot_acc2taxid --out databases
# The PDB accession to taxonomy ID mapping file
get_db --db_name pdb_acc2taxid --out databases
# The NCBI taxonomy database
get_db --db_name taxdb --out databasesNow that we have the databases downloaded, we can use taxonize_gb to filter the nr FASTA to keep only the plant protein records:
# we use the taxid of Viridiplantae (33090) and we write the outputs to a directory "plant_nr"
taxonize_gb --db nr --db_path databases/nr.gz --taxdb databases/taxdump.tar.gz --prot_acc2taxid databases/prot.accession2taxid.gz --pdb_acc2taxid pdb.accession2taxid.gz --taxid 33090 --out plant_nr- Insects non-redundant nucleotide database
Similar to the previous example, we first need to use the get_db to download the database file:
# The nt FASTA file
get_db --db_name nt --out databases
# The GenBank accession to taxonomy ID mapping file
get_db --db_name nucl_gb_acc2taxid --out databases
# The WGS accession to taxonomy ID mapping file
get_db --db_name nucl_wgs_acc2taxid --out databases
# The NCBI taxonomy database
get_db --db_name taxdb --out databasesNow we can use the taxonize_gb to filter the nt FASTA to keep only the insects nucleotide records:
# we use the taxid of Insecta (50557) and we write the outputs to a directory "insects_nt"
taxonize_gb --db nt --db_path databases/nt.gz --taxdb databases/taxdump.tar.gz --nucl_gb_acc2taxid databases/nucl_gb.accession2taxid.gz --nucl_wgs_acc2taxid databases/nucl_wgs.accession2taxid.gz --taxid 50557 --out insect_nt- Nematodes mitochondrial genomes
We can use the databases we downloaded in the previous steps, then we can proceed to the next step to use the taxonize_db with the flag --keywords mitochondrion,'complete genome' to find the header that contain both words, as follow:
# we use the taxid of Nematoda (6231) and we write the outputs to a directory "nematoda_mito"
taxonize_gb --db nt --db_path databases/nt.gz --taxdb databases/taxdump.tar.gz --nucl_gb_acc2taxid databases/nucl_gb.accession2taxid.gz --nucl_wgs_acc2taxid databases/nucl_wgs.accession2taxid.gz --taxid 6231 --keywords mitochondrion,'complete genome' --out nematoda_mitoThis package is distributed under the Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0). Please see the LICENSE file for the full license text.