genome_collector 0.1.3

Easily download and store genomes and BLAST DBs from NCBI

Genome Collector is a Python library to download and manage reference genome data for specific TaxIDs, in particular nucleotide and protein sequences (in fasta/genbank/gff formats), and alignment databases (BLAST, Bowtie1/2).

The data is downloaded automatically on a need-to basis, making it very easy for Python projects to use and re-use reference genomes of E. coli, S. cerevisiae, and so on, without the worry of manually downloading from NCBI.

Examples

Let’s get Biopython records of all protein sequences in E. coli:

from genome_collector import GenomeCollection
collection = GenomeCollection()
records = collection.get_taxid_biopython_records(511145, "protein_fasta")

And that’s it! If the protein data wasn’t already on your machine, Genome Collector downloaded from NCBI, and stored in your “collection” for the next time time you need it.

Now let’s get a path to a local BLAST database for S. cerevisiae:

from genome_collector import GenomeCollection
collection = GenomeCollection()
db_path = collection.get_taxid_blastdb_path(taxid=559292, db_type='nucl')

If there was no cerevisiae database on your machine, Genome Collector downloaded the genome data and built it. It is now in your collection, and you can use the returned db_path to start a BLAST process:

import subprocess
process = subprocess.run([
    'blastn', '-db', db_path, '-query', 'queries.fa', '-out', 'results.txt'
])

Infos

• Installation: with pip install genome_collector. Some BLAST and Bowtie features also require specific software installed, see docs.

• Docs: https://edinburgh-genome-foundry.github.io/genome_collector/

• Github repo: released on Github https://github.com/Edinburgh-Genome-Foundry/genome_collector

• Licence: MIT

• Similar software: see pre-existing projects ncbi-genome-download and Genomepy . In comparison, Genome Collector is more opinionated, it uses TaxID first and has features like on-demand genome downloading and database building, and Biopython records loading.

Everyone is welcome to contribute !

More biology software

Genome Collector is part of the EGF Codons synthetic biology software suite for DNA design, manufacturing and validation.