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GenBank Loader Example
A small set of real GenBank flat files from NCBI, provided as a runnable example
for the datasets GenBank packaged loader (see
huggingface/datasets#7951).
Each file is a complete, unmodified GenBank record fetched from the NCBI Nucleotide database via E-utilities. One file is stored gzipped to demonstrate that the loader reads compressed inputs transparently.
Contents
| File | Accession | Organism | Length (bp) | Note |
|---|---|---|---|---|
U49845.gb |
U49845 | Saccharomyces cerevisiae | 5,028 | plain |
V00662.gb.gz |
V00662 | Homo sapiens (mitochondrion) | 16,569 | gzipped |
X04370.gb |
X04370 | Human herpesvirus 3 | 124,884 | plain |
Usage
from datasets import load_dataset
# Load every GenBank file in the repo
ds = load_dataset("ermiaazarkhalili/datasets-genbank-test", data_files="*.gb*", split="train")
print(ds[0]["locus_name"], ds[0]["organism"], ds[0]["length"])
# The FEATURES section is decoded into structured objects via the Json() feature:
print(ds[0]["features"][0])
Columns: locus_name, accession, version, definition, organism, taxonomy,
keywords, sequence, features, length, molecule_type.
Provenance
Records retrieved from NCBI Nucleotide (efetch, rettype=gb). GenBank data is a work
of the U.S. Government / NCBI; individual sequence submissions retain their submitters'
rights. This repository is intended solely as a loader example/test fixture.
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