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MIDORI2

MIDORI2 provides quality-controlled, QIIME-formatted mitochondrial reference files built from GenBank. Releases are static, so biodbs builds the download URL from the gene, version, and options. Each gene has a .fasta.gz sequence file and a matching .taxon.gz taxonomy sidecar.

Download a File

from biodbs.fetch.MIDORI2 import MIDORI2_Fetcher

fetcher = MIDORI2_Fetcher()
version = "GenBank271_2026-04-07"  # full version string

seqs = fetcher.download("CO1", dest="data/midori2", version=version)
taxa = fetcher.download("CO1", dest="data/midori2", version=version, kind="taxon")

Options:

  • kind: "fasta" (sequences, default) or "taxon" (taxonomy sidecar)
  • unique: True for the unique set (default), False for longest
  • species: True for species-level (QIIME_sp) files

Just the URL

url = fetcher.build_url("srRNA", version, species=True)

Convenience Functions

from biodbs.fetch import midori2_download, midori2_build_url

path = midori2_download("CO1", dest="data/midori2", version="GenBank271_2026-04-07")
url = midori2_build_url("CO1", "GenBank271_2026-04-07", kind="taxon")

The version is the full GenBankNNN_YYYY-MM-DD string; check reference-midori.info for the current release.