gene-fetch 1.0.6

Gene Fetch: High-throughput NCBI Sequence Retrieval Tool

Gene Fetch

Gene Fetch enables high-throughput retreival of sequence data from NCBI databases based on taxonomy IDs (taxids) or taxonomic heirarchies. It can retrieve both protein and/or nucleotide sequences for various genes, including protein-coding genes (e.g., cox1, cytb, rbcl, matk) and rRNA genes (e.g., 16S, 18S).

Installation:

Install from PyPI

pip install gene-fetch

Post-instllation testing:

• The Gene Fetch package includes comprehensive tests - Testing is divided into basic tests (which don't require external API access) and integration tests (which may require NCBI API credentials). Install pytest:

pip install pytest

Run basic tests:

pytest

• This will take a few minutes to run 65 tests, consisting of 8 test modules (tests/test_*.py). You will get 1 warning regarding API credentials as these are not provided in the basic tests.

Usage:

python gene_fetch.py -g/--gene <gene_name> --type <sequence_type> -i/--in <samples.csv> -o/--out <output_directory> 

--h/--help: Show help and exit.

Required arguments:

-g/--gene: Name of gene to search for in NCBI GenBank database (e.g., cox1/16s/rbcl). --type: Sequence type to fetch; 'protein', 'nucleotide', or 'both' ('both' will initially search and fetch a protein sequence, and then fetches the corresponding nucleotide CDS for that protein sequence). -i/--in: Path to input CSV file containing sample IDs and TaxIDs (see Input section below). i2/--in2: Path to alternative input CSV file containing sample IDs and taxonomic information for each sample (see Input section below). o/--out: Path to output directory. The directory will be created if it does not exist. e/--email and -k/--api-key: Email address and associated API key for NCBI account. An NCBI account is required to run this tool (due to otherwise strict API limitations) - information on how to create an NCBI account and find your API key can be found here.

Optional arguments:

--protein-size: Minimum protein sequence length filter. Applicable to mode 'batch' and 'single' search modes (default: 500). --nucleotide-size: Minimum nucleotide sequence length filter. Applicable to mode 'batch' and 'single' search modes (default: 1500). s/--single: Taxonomic ID for 'single' sequence search mode (-i and -i2 are ignored when run with -s mode). 'single' mode will fetch all (or N if specifying --max-sequences) target gene or protein sequences on GenBank for a specific taxonomic ID. --max-sequences: Maximum number of sequences to fetch for a specific taxonomic ID (only applies when run in 'single' mode). -b/--genbank: Saves genbank (.gb) files for fetched nucleotide and/or protein sequences to genbank/ (applies when run in 'batch' or 'single' mode).

Input:

Example 'samples.csv' input file (-i/--in)

ID	taxid
sample-1	177658
sample-2	177627
sample-3	3084599

Example 'samples_taxonomy.csv' input file (-i2/--in2)

ID	phylum	class	order	family	genus	species
sample-1	Arthropoda	Insecta	Diptera	Acroceridae	Astomella
sample-2	Arthropoda	Insecta	Hemiptera	Cicadellidae	Psammotettix	Psammotettix sabulicola
sample-3	Arthropoda	Insecta	Trichoptera	Limnephilidae	Dicosmoecus	Dicosmoecus palatus

• Leave blank if taxonomic information not known/needed

Authored by Dan Parsons and Ben Price @ NHMUK (2025).