Taxonize_genbank

Taxonize_genbank is a Python package designed to simplify the process of downloading, filtering, and curating GenBank's non-redundant protein and nucleotide databases based on taxonomy IDs (TaxIDs) and/or specific keywords. This tool is particularly useful for researchers working with large-scale genomic datasets who need to extract specific subsets of data.

The tool supports advanced filtering options, allowing users to:

• Include Multiple TaxIDs: Extract sequences associated with multiple taxa by specifying a list of TaxIDs.
• Exclude Specific TaxIDs: Remove unwanted or contaminant taxa from the dataset during filtering.

These features make Taxonize_genbank highly flexible and customizable for a variety of research applications.

Features

• Download NCBI databases, including taxonomy, protein, and nucleotide datasets.
• Filter GenBank's non-redundant databases (nr or nt) by taxonomy ID or keywords.
• Retrieve taxonomic lineages for FASTA accessions.
• Support for advanced filtering using multiple TaxIDs or excluding specific TaxIDs.

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Installation

Prerequisites

Ensure you have the following dependencies 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
• isal:1.7.1

Installation Steps

1. Clone the Repository
   Clone the GitHub repository to your local machine:

git clone https://github.com/msabrysarhan/taxonize_genbank

2. Install via pip (Recommended)
   Alternatively, install taxonize_gb directly using pip:

pip install taxonize-gb

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Usage

The Taxonize_genbank package includes three main modules:

1. get_db.py: Download NCBI Databases

This module allows you to download NCBI databases required for filtering.

Command:

get_db.py --db_name <DB_NAME> --out <OUTPUT_DIRECTORY>

Options:

• --db_name: Specify the database to download (e.g., taxdb, nr, nt, etc.).
• --out: Path to the output directory where the database will be stored.

Example:

Download the non-redundant protein database (nr):

get_db.py --db_name nr --out databases/

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2. taxonize_gb.py: Filter Databases by TaxID or Keywords

This module filters the downloaded database based on taxonomy ID or keywords.

Command:

taxonize_gb.py --db <DB> --db_path <DB_PATH> [OPTIONS] --out <OUTPUT_DIRECTORY>

Required Arguments:

• --db: Specify the database type (nt for nucleotide or nr for protein).
• --db_path: Path to the gzipped FASTA file (if not provided, it will be downloaded automatically).
• --out: Path to the output directory.

Optional Arguments:

• --taxid: Target taxonomy ID to filter for.
• --keywords: Keywords to include in FASTA headers.
• Additional arguments for mapping files (--prot_acc2taxid, --nucl_gb_acc2taxid, etc.).

Example:

Filter the non-redundant protein database (nr) for plant proteins (TaxID: 33090):

taxonize_gb.py --db nr --db_path databases/nr.gz
--taxdb databases/taxdump.tar.gz
--prot_acc2taxid databases/prot.accession2taxid.gz
--pdb_acc2taxid databases/pdb.accession2taxid.gz
--taxid 33090
--out plant_nr/

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3. get_taxonomy.py: Retrieve Taxonomic Lineages

This module extracts taxonomic lineages from GenBank FASTA files.

Command:

get_taxonomy.py --fasta <FASTA_FILE> --map <MAPPING_FILE> --out <OUTPUT_FILE>

Options:

• --fasta: Path to the FASTA file.
• --map: Path to the mapping file (e.g., accession-to-taxonomy mapping).
• --out: Path to save the output file.

Example:

Retrieve taxonomic lineages from a FASTA file:

get_taxonomy.py --fasta input.fasta
--map databases/prot.accession2taxid.gz
--out taxonomy_lineages.txt

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Examples

Example 1: Plant Non-redundant Protein Database

1. Download required files:

get_db.py --db_name nr --out databases/
get_db.py --db_name prot_acc2taxid --out databases/
get_db.py --db_name pdb_acc2taxid --out databases/
get_db.py --db_name taxdb --out databases/

2. Filter for plant proteins (TaxID: 33090):

taxonize_gb.py --db nr
--db_path databases/nr.gz
--taxdb databases/taxdump.tar.gz
--prot_acc2taxid databases/prot.accession2taxid.gz
--pdb_acc2taxid databases/pdb.accession2taxid.gz
--taxid 33090
--out plant_nr/

Example 2: Insect Non-redundant Nucleotide Database

1. Download required files:

get_db.py --db_name nt --out databases/
get_db.py --db_name nucl_gb_acc2taxid --out databases/
get_db.py --db_name nucl_wgs_acc2taxid --out databases/
get_db.py --db_name taxdb --out databases/

2. Filter for insect nucleotides (TaxID: 50557):

taxonize_gb.py --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/

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License

This project is licensed under the MIT License.
See the LICENSE file for full details.