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bedrock.bio

refseq.structural_features

import bedrock_bio as bb

rel = bb.load_table('refseq.structural_features')
rel = rel.filter("assembly_accession = 'GCF_000001405.25'")

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
sources assembly_accession sequence_accession start end is_forward_strand structural_feature_id structural_type annotation_method note
0 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_012920.1 16024 17145 False id-NC_012920.1:1..16569 D_loop RefSeq None

Description

Section titled “Description”

RefSeq structural sequence element intervals, one row per interval.

Partitions

Section titled “Partitions”
  • assembly_accession
    • 'GCF_000001405.25'
    • 'GCF_000001405.40'
    • 'GCF_000001635.20'
    • 'GCF_000001635.27'
    • 'GCF_000001895.5'
    • 'GCF_000002035.5'
    • 'GCF_000002035.6'
    • 'GCF_000002285.3'
    • 'GCF_000002285.5'
    • 'GCF_000003025.5'
    • 'GCF_000003025.6'
    • 'GCF_000003625.3'
    • 'GCF_000004195.4'
    • 'GCF_000146045.2'
    • 'GCF_000151735.1'
    • 'GCF_000182965.3'
    • 'GCF_000215625.1'
    • 'GCF_000349665.1'
    • 'GCF_000364345.1'
    • 'GCF_001704415.1'
    • 'GCF_001704415.2'
    • 'GCF_001858045.2'
    • 'GCF_002263795.3'
    • 'GCF_003339765.1'
    • 'GCF_008728515.1'
    • 'GCF_011764305.1'
    • 'GCF_016699485.2'
    • 'GCF_017654675.1'
    • 'GCF_052040795.1'

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 nucleotide sequence accession on which the structural feature is annotated; joins refseq.assembly_sequences.sequence_accession.
start INT 1-based inclusive start coordinate of the structural feature interval on sequence_accession.
end INT 1-based inclusive end coordinate of the structural feature interval on sequence_accession.
is_forward_strand BOOLEAN Whether the structural feature interval is on the forward strand; null when the GFF strand is unspecified.
structural_feature_id TEXT Local GFF3 ID of the structural feature; not a stable RefSeq identifier.
structural_type TEXT Source GFF3 structural feature type.
annotation_method TEXT NCBI GFF column-2 annotation method or source, if supplied.
note TEXT Free text GFF Note annotation, if supplied.