README.md

metadata

pretty_name: BFD Source Archive Index
license: other
tags:
  - biology
  - protein
  - sequence-database
  - bfd
  - fasta
  - archive
  - parquet
configs:
  - config_name: default
    data_files:
      - split: train
        path: data/train-*.parquet
      - split: test
        path: data/test-*.parquet

BFD Source Archive Index

BFD is a very large clustered protein sequence database built from UniProt and metagenomic sequence resources, commonly used for homology search and multiple sequence alignment generation.

Splits

The split is deterministic by chunk identifier: sha256(index_id) % 10. Bucket 0 is test; buckets 1 through 9 are train.

Split	Rows
train	255
test	17
total	272

Source File

File	Size
bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz	291,649,557,441 bytes

Usage

pip install datasets

Load the archive index:

from datasets import load_dataset

ds = load_dataset("LiteFold/BFD")
print(ds)
print(ds["train"][0])

Load one split:

from datasets import load_dataset

train = load_dataset("LiteFold/BFD", split="train")
test = load_dataset("LiteFold/BFD", split="test")

Download the original archive:

from huggingface_hub import hf_hub_download

archive_path = hf_hub_download(
    repo_id="LiteFold/BFD",
    repo_type="dataset",
    filename="bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz",
)

Load the source-file manifest:

import pandas as pd
from huggingface_hub import hf_hub_download

path = hf_hub_download(
    repo_id="LiteFold/BFD",
    repo_type="dataset",
    filename="metadata/source_files.parquet",
)
source_files = pd.read_parquet(path)
print(source_files)

Columns

Column	Description
index_id	Stable row ID for one compressed chunk.
repo_id	Hugging Face dataset repository.
source_file	Source archive filename.
source_sha	Source repository commit used to build the index.
source_format	Source archive format.
chunk_index	Zero-based compressed chunk index.
byte_start	Inclusive compressed byte offset.
byte_end_exclusive	Exclusive compressed byte offset.
chunk_size_bytes	Compressed chunk size in bytes.
total_size_bytes	Full compressed archive size.
chunk_size_gib	Target chunk size in GiB.
is_first_chunk	Whether the row indexes the first chunk.
is_last_chunk	Whether the row indexes the final chunk.
access_note	Note describing the index scope.
split_bucket	Deterministic split bucket from sha256(index_id) % 10.

Citation

@article{steinegger2019bfd,
  title   = {Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold},
  author  = {Steinegger, Martin and Mirdita, Milot and S{\"o}ding, Johannes},
  journal = {Nature Methods},
  volume  = {16},
  pages   = {603--606},
  year    = {2019},
  doi     = {10.1038/s41592-019-0437-4}
}