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bedrock.bio

ensembl.dna_sequences

import bedrock_bio as bb

rel = bb.load_table('ensembl.dna_sequences')
rel = rel.filter("genbank_assembly_accession = 'GCA_000001215.4'")

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
sources release genbank_assembly_accession sequence_id position nucleotide is_masked
0 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 2L 1 C True
1 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 2L 2 G True
2 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 2L 3 A True
3 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 2L 4 C True
4 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 2L 5 A True

Description

Section titled “Description”

Individual nucleotide positions in Ensembl’s soft-masked top-level genomic DNA FASTA.

One row per 1-based position in Ensembl’s dna_sm.toplevel FASTA, covering every sequence Ensembl marks as top-level, including chromosomes, non-chromosomal sequences, and padded haplotype or patch sequences.

Always filter on genbank_assembly_accession, sequence_id, and a position interval. sequence_id joins the raw Ensembl GFF3 coordinate system.

Partitions

Section titled “Partitions”
  • genbank_assembly_accession
    • 'GCA_000001215.4'
    • 'GCA_000001405.29'
    • 'GCA_000001635.9'
    • 'GCA_000001735.1'
    • 'GCA_000002035.4'
    • 'GCA_000002285.4'
    • 'GCA_000002525.1'
    • 'GCA_000002655.1'
    • 'GCA_000002765.3'
    • 'GCA_000002855.2'
    • 'GCA_000002945.2'
    • 'GCA_000002985.3'
    • 'GCA_000003025.6'
    • 'GCA_000003195.3'
    • 'GCA_000003625.1'
    • 'GCA_000004195.4'
    • 'GCA_000004515.4'
    • 'GCA_000005845.2'
    • 'GCA_000006565.2'
    • 'GCA_000006665.1'
    • 'GCA_000006745.1'
    • 'GCA_000006765.1'
    • 'GCA_000006845.1'
    • 'GCA_000006885.1'
    • 'GCA_000006925.2'
    • 'GCA_000006945.2'
    • 'GCA_000007545.1'
    • 'GCA_000007565.2'
    • 'GCA_000007785.1'
    • 'GCA_000008525.1'
    • 'GCA_000008765.1'
    • 'GCA_000008805.1'
    • 'GCA_000009045.1'
    • 'GCA_000009085.1'
    • 'GCA_000009205.2'
    • 'GCA_000011065.1'
    • 'GCA_000011325.1'
    • 'GCA_000013425.1'
    • 'GCA_000013465.1'
    • 'GCA_000015005.1'
    • 'GCA_000016305.1'
    • 'GCA_000025565.1'
    • 'GCA_000025985.1'
    • 'GCA_000027005.1'
    • 'GCA_000027305.1'
    • 'GCA_000146045.2'
    • 'GCA_000149245.3'
    • 'GCA_000151735.1'
    • 'GCA_000167675.2'
    • 'GCA_000174395.2'
    • 'GCA_000182965.3'
    • 'GCA_000196035.1'
    • 'GCA_000196095.1'
    • 'GCA_000215625.1'
    • 'GCA_000226075.1'
    • 'GCA_000237925.3'
    • 'GCA_000285655.3'
    • 'GCA_000306945.1'
    • 'GCA_000349665.1'
    • 'GCA_000409795.2'
    • 'GCA_000805365.1'
    • 'GCA_001433935.1'
    • 'GCA_001457595.1'
    • 'GCA_001704415.1'
    • 'GCA_001858045.3'
    • 'GCA_002263795.4'
    • 'GCA_002863925.1'
    • 'GCA_003339765.3'
    • 'GCA_003668045.2'
    • 'GCA_008728515.1'
    • 'GCA_011100615.1'
    • 'GCA_016699485.1'
    • 'GCA_016772045.2'
    • 'GCA_018294505.1'
    • 'GCA_036323735.1'
    • 'GCA_902167145.1'
    • 'GCA_905237065.2'

Schema

Section titled “Schema”
Column Type Description
sources STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[] Provenance for the Ensembl FASTA file.
release TEXT Ensembl release number the FASTA was drawn from.
genbank_assembly_accession TEXT Partition column. GenBank assembly accession.
sequence_id TEXT Ensembl top-level FASTA record identifier, matching the GFF3 sequence ID.
position INT 1-based nucleotide position on sequence_id.
nucleotide TEXT Uppercase IUPAC DNA nucleotide code at position.
is_masked BOOLEAN Whether the nucleotide is soft-masked in the source FASTA, indicated by a lowercase base.