NCBI and Sequence Retrieval

Download NCBI datasets and prepare GenBank records for downstream workflows.

Sequence analysis starts with the correct source data. OrthoEvolution provides FTP and GenBank helpers that retrieve sequence data and prepare analysis inputs. Some downloads are large, and all remote downloads depend on NCBI services.

Download a BLAST database

from pathlib import Path

from OrthoEvol.Tools.ftp import NcbiFTPClient

download_path = Path("databases") / "NCBI" / "blast" / "db"
ncbi_ftp = NcbiFTPClient(
    email="researcher@example.org",
    max_workers=4,
)

try:
    ncbi_ftp.getblastdb(
        database_name="refseq_rna",
        download_path=download_path,
        v5=True,
        extract=True,
    )
finally:
    ncbi_ftp.close_connection()

Before you start the transfer, choose a destination with enough storage. If a transfer stops, make sure that the files are complete before you use them.

Version 5 selections use NCBI metadata to match the exact database. The client downloads every volume in that selection. It compares each archive with its MD5 checksum before extraction. It then keeps the checksum sidecar as an installation marker. A repeated request can reuse an installation that passed these tests.

Download a RefSeq release selection

from pathlib import Path

from OrthoEvol.Tools.ftp import NcbiFTPClient

download_path = Path("databases") / "NCBI" / "refseq" / "release"
ncbi_ftp = NcbiFTPClient(
    email="researcher@example.org",
    max_workers=4,
)

try:
    ncbi_ftp.getrefseqrelease(
        collection_subset="vertebrate_mammalian",
        seqtype="rna",
        seqformat="gbff",
        download_path=download_path,
        extract=True,
    )
finally:
    ncbi_ftp.close_connection()

This request downloads RNA GenBank flat files for the vertebrate-mammalian collection. A local marker records the NCBI release number and selected files. The client skips a later request only if the marker and output files match the current release.

Common sequence formats include:

Extension	Typical content
.fna	Genomic or other nucleotide FASTA sequences
.ffn	Nucleotide FASTA sequences for coding regions
.faa	Protein FASTA sequences
.frn	Non-coding RNA FASTA sequences
.gbff	GenBank flat-file records with sequence annotations

Select seqtype and seqformat for the exact NCBI collection that you need. A valid file format does not show that the release, molecule type, or taxa fit your analysis.

GenBank processing

The GenBank class connects a project to local GenBank archives and BioSQL resources. GenBank records contain sequences and their annotations. The class can:

• Locate accessions in a local GenBank database
• Write individual GenBank records
• Extract nucleotide or protein FASTA files
• Organize outputs by gene and organism

Before you create the class, make sure that the project paths and required database resources exist. Several methods use NCBI database locations from a managed repository.

Record what you downloaded

Record the NCBI database name and its release or retrieval date. Also record the available file checksums and the accession-table version. NCBI content can change without an OrthoEvolution release. The package version alone cannot reproduce a retrieval.

When retrieval does not complete

First identify which part of the retrieval stopped. The cause can be a network interruption, a missing remote file, insufficient storage, a checksum mismatch, or an incomplete BioSQL setup. Do not use a partial archive. A file at the destination is not proof of a complete transfer.