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bedrock.bio

refseq.dna_sequences

import bedrock_bio as bb

rel = bb.load_table('refseq.dna_sequences')
rel = rel.filter("assembly_accession = 'GCF_000001215.4'")

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
sources assembly_accession sequence_accession position nucleotide is_masked
0 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_004354.4 1 G False
1 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_004354.4 2 A False
2 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_004354.4 3 A False
3 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_004354.4 4 T False
4 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_004354.4 5 T False

Description

Section titled “Description”

Individual nucleotide positions in RefSeq genomic FASTA sequences.

Each row represents one 1-based position.

Nucleotide codes are uppercase IUPAC values; is_masked retains soft-masking information.

Partitions

Section titled “Partitions”
  • assembly_accession
    • 'GCF_000001215.4'
    • 'GCF_000001405.25'
    • 'GCF_000001405.40'
    • 'GCF_000001635.20'
    • 'GCF_000001635.27'
    • 'GCF_000001735.3'
    • 'GCF_000001735.4'
    • 'GCF_000001895.5'
    • 'GCF_000002035.5'
    • 'GCF_000002035.6'
    • 'GCF_000002285.5'
    • 'GCF_000002525.2'
    • 'GCF_000002655.1'
    • 'GCF_000002765.6'
    • 'GCF_000002855.4'
    • 'GCF_000002945.1'
    • 'GCF_000002945.2'
    • 'GCF_000002985.6'
    • 'GCF_000003025.5'
    • 'GCF_000003025.6'
    • 'GCF_000003195.3'
    • 'GCF_000003625.3'
    • 'GCF_000004195.4'
    • 'GCF_000004515.5'
    • 'GCF_000004515.6'
    • 'GCF_000005845.2'
    • 'GCF_000006565.2'
    • 'GCF_000006665.1'
    • 'GCF_000006745.1'
    • 'GCF_000006765.1'
    • 'GCF_000006845.1'
    • 'GCF_000006885.1'
    • 'GCF_000006925.2'
    • 'GCF_000006945.2'
    • 'GCF_000007545.1'
    • 'GCF_000007565.2'
    • 'GCF_000007785.1'
    • 'GCF_000008525.1'
    • 'GCF_000008765.1'
    • 'GCF_000008805.1'
    • 'GCF_000009045.1'
    • 'GCF_000009085.1'
    • 'GCF_000009205.2'
    • 'GCF_000011065.1'
    • 'GCF_000011325.1'
    • 'GCF_000013425.1'
    • 'GCF_000013465.1'
    • 'GCF_000015005.1'
    • 'GCF_000016305.1'
    • 'GCF_000025565.1'
    • 'GCF_000025985.1'
    • 'GCF_000027005.1'
    • 'GCF_000027305.1'
    • 'GCF_000146045.2'
    • 'GCF_000149245.1'
    • 'GCF_000151735.1'
    • 'GCF_000167675.1'
    • 'GCF_000174395.2'
    • 'GCF_000182965.3'
    • 'GCF_000188115.5'
    • 'GCF_000195715.1'
    • 'GCF_000195955.2'
    • 'GCF_000195995.1'
    • 'GCF_000196035.1'
    • 'GCF_000196095.1'
    • 'GCF_000203835.1'
    • 'GCF_000215625.1'
    • 'GCF_000226075.1'
    • 'GCF_000237925.1'
    • 'GCF_000285655.3'
    • 'GCF_000306945.1'
    • 'GCF_000349665.1'
    • 'GCF_000364345.1'
    • 'GCF_000409795.2'
    • 'GCF_000767705.1'
    • 'GCF_000805365.1'
    • 'GCF_001077675.1'
    • 'GCF_001433935.1'
    • 'GCF_001457595.1'
    • 'GCF_001593425.2'
    • 'GCF_001704415.1'
    • 'GCF_001704415.2'
    • 'GCF_001858045.2'
    • 'GCF_002263795.3'
    • 'GCF_002759435.1'
    • 'GCF_002863925.1'
    • 'GCF_003339765.1'
    • 'GCF_003668045.3'
    • 'GCF_007990345.1'
    • 'GCF_008728515.1'
    • 'GCF_009914755.1'
    • 'GCF_011764305.1'
    • 'GCF_016699485.2'
    • 'GCF_016772045.2'
    • 'GCF_017654675.1'
    • 'GCF_018294505.1'
    • 'GCF_020379485.1'
    • 'GCF_034190915.1'
    • 'GCF_036323735.1'
    • 'GCF_037993035.2'
    • 'GCF_047675955.1'
    • 'GCF_049350105.2'
    • 'GCF_049354715.1'
    • 'GCF_052040795.1'
    • 'GCF_054392235.1'
    • 'GCF_902167145.1'
    • 'GCF_905237065.1'
    • 'GCF_964237555.1'

Schema

Section titled “Schema”
Column Type Description
sources STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[] Source provenance for the row.
assembly_accession TEXT Partition column. Versioned RefSeq assembly accession (GCF accession).
sequence_accession TEXT Versioned RefSeq accession of the genomic sequence; joins refseq.assembly_sequences.sequence_accession.
position INT 1-based nucleotide position on sequence_accession.
nucleotide TEXT Uppercase IUPAC DNA nucleotide code at position.
is_masked BOOLEAN Whether the nucleotide is soft-masked in the source RefSeq genomic FASTA, indicated by a lowercase base.