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bedrock.bio

ensembl.cds

import bedrock_bio as bb

rel = bb.load_table('ensembl.cds')
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 transcript_id protein_id protein_version sequence_id start_position end_position is_forward_strand phase cds_source
0 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBtr0005088 FBpp0099974 <NA> 2L 8366311 8366394 True 0 FlyBase
1 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBtr0005088 FBpp0099974 <NA> 2L 8367096 8367249 True 0 FlyBase
2 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBtr0005088 FBpp0099974 <NA> 2L 8367312 8367730 True 2 FlyBase
3 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBtr0005088 FBpp0099974 <NA> 2L 8367797 8367871 True 0 FlyBase
4 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBtr0005088 FBpp0099974 <NA> 2L 8367931 8368696 True 0 FlyBase

Description

Section titled “Description”

Coding sequence (CDS) annotation — translated exon segments and their Ensembl protein IDs.

One row per (transcript, CDS segment).

Always filter on genbank_assembly_accession. protein_id is the Ensembl protein the CDS translates to.

Join to transcripts on transcript_id.

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 GFF3 feature records.
release TEXT Ensembl release number the annotation was drawn from.
genbank_assembly_accession TEXT Partition column. GenBank assembly accession.
transcript_id TEXT Ensembl transcript ID this CDS belongs to.
protein_id TEXT Ensembl protein ID the CDS translates to (e.g. ENSP00000123456).
protein_version INT Version suffix of the protein ID. May be null.
sequence_id TEXT GFF3 sequence ID the CDS is located on.
start_position INT 1-based start coordinate of the CDS segment.
end_position INT 1-based end coordinate of the CDS segment.
is_forward_strand BOOLEAN Whether the CDS is on the forward strand.
phase Int8 GFF3 CDS reading-frame phase (0, 1, or 2).
cds_source TEXT Annotation source in GFF3 column 2 (e.g. ensembl, havana, ensembl_havana).