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bedrock.bio

ensembl.regions

import bedrock_bio as bb

rel = bb.load_table('ensembl.regions')
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 region_type start_position end_position score is_forward_strand region_source aliases is_circular external_name analysis_name
0 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 211000022278031 region 1 1021 NaN <NA> BDGP6.54 [DS485919, NW_001847208, 211000022278031, DS48... <NA> None None
1 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 211000022278032 region 1 6936 NaN <NA> BDGP6.54 [DS483755, NW_001845044, 211000022278032, DS48... <NA> None None
2 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 211000022278033 region 1 1143 NaN <NA> BDGP6.54 [DS485425, NW_001846714, 211000022278033, DS48... <NA> None None
3 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 211000022278038 region 1 1395 NaN <NA> BDGP6.54 [DS484861, NW_001846150, 211000022278038, DS48... <NA> None None
4 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 211000022278047 region 1 2020 NaN <NA> BDGP6.54 [DS484484, NW_001845773, 211000022278047, DS48... <NA> None None

Description

Section titled “Description”

Assembly and biologically annotated regions from Ensembl GFF3.

One row per biological_region, region, scaffold, or supercontig feature.

Always filter on genbank_assembly_accession. sequence_id may be a chromosome, scaffold, contig, or other assembly sequence; use region_type to distinguish the source feature type.

Partitions

Section titled “Partitions”
  • genbank_assembly_accession
    • 'GCA_000001215.4'
    • 'GCA_000001405.29'
    • 'GCA_000001635.9'
    • 'GCA_000002035.4'
    • 'GCA_000002285.4'
    • 'GCA_000002525.1'
    • 'GCA_000002655.1'
    • 'GCA_000002765.3'
    • 'GCA_000002855.2'
    • 'GCA_000002945.2'
    • '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_000006765.1'
    • 'GCA_000006845.1'
    • 'GCA_000006925.2'
    • 'GCA_000006945.2'
    • 'GCA_000007545.1'
    • 'GCA_000007565.2'
    • 'GCA_000007785.1'
    • '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_000149245.3'
    • 'GCA_000151735.1'
    • 'GCA_000167675.2'
    • 'GCA_000174395.2'
    • 'GCA_000182965.3'
    • 'GCA_000196035.1'
    • 'GCA_000196095.1'
    • 'GCA_000215625.1'
    • '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 GFF3 feature records.
release TEXT Ensembl release number the annotation was drawn from.
genbank_assembly_accession TEXT Partition column. GenBank assembly accession.
sequence_id TEXT GFF3 sequence ID on which the region is located.
region_type TEXT Raw GFF3 feature type — biological_region, region, scaffold, or supercontig.
start_position INT 1-based start coordinate of the region.
end_position INT 1-based end coordinate of the region.
score DOUBLE Numeric GFF3 feature score, if supplied. May be null.
is_forward_strand BOOLEAN Whether the region is on the forward strand. May be null when GFF3 strand is unspecified.
region_source TEXT Annotation source in GFF3 column 2. May be null.
aliases TEXT[] Alternate sequence names from the comma-separated GFF3 Alias attribute; empty when not supplied.
is_circular BOOLEAN Whether the GFF3 Is_circular attribute marks the region as circular. May be null when the attribute is absent.
external_name TEXT Biological-region external name from GFF3 external_name, if supplied. May be null.
analysis_name TEXT Ensembl analysis name from GFF3 logic_name, if supplied. May be null.