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bedrock.bio

refseq.repeat_features

import bedrock_bio as bb

rel = bb.load_table('refseq.repeat_features')
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 start end is_forward_strand repeat_feature_id repeat_type annotation_method db_xrefs ... repeat_unit_sequence repeat_unit_range satellite_type mobile_element_type function experiments is_partial is_start_partial is_end_partial note
0 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_004353.4 5057 5194 True id-NC_004353.4:5057..5194 mobile_genetic_element RefSeq [{'db': 'FLYBASE', 'id': 'FBti0062196'}] ... None None None transposon:INE-1{}4135 None [] False False False None
1 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_004353.4 5464 5498 True id-NC_004353.4:5464..5498 mobile_genetic_element RefSeq [{'db': 'FLYBASE', 'id': 'FBti0062197'}] ... None None None transposon:INE-1{}4136 None [] False False False None
2 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_004353.4 11838 11975 True id-NC_004353.4:11838..11975 mobile_genetic_element RefSeq [{'db': 'FLYBASE', 'id': 'FBti0062198'}] ... None None None transposon:INE-1{}4137 None [] False False False None
3 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_004353.4 12245 12279 True id-NC_004353.4:12245..12279 mobile_genetic_element RefSeq [{'db': 'FLYBASE', 'id': 'FBti0062199'}] ... None None None transposon:INE-1{}4138 None [] False False False None
4 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_004353.4 13649 20086 True id-NC_004353.4:13649..20086 mobile_genetic_element RefSeq [{'db': 'FLYBASE', 'id': 'FBti0020402'}] ... None None None transposon:McClintock{}1478 None [] False False False None

Description

Section titled “Description”

RefSeq repeat intervals, one row per interval. repeat_type classifies each interval, while repeat unit and mobile element fields describe repeat subclasses when supplied.

Partitions

Section titled “Partitions”
  • assembly_accession
    • 'GCF_000001215.4'
    • 'GCF_000001405.25'
    • 'GCF_000001405.40'
    • 'GCF_000001635.27'
    • 'GCF_000001735.3'
    • 'GCF_000001735.4'
    • 'GCF_000002525.2'
    • 'GCF_000002855.4'
    • 'GCF_000003025.5'
    • 'GCF_000003025.6'
    • 'GCF_000003195.3'
    • 'GCF_000003625.3'
    • 'GCF_000005845.2'
    • 'GCF_000006925.2'
    • 'GCF_000006945.2'
    • 'GCF_000007545.1'
    • 'GCF_000009085.1'
    • 'GCF_000009205.2'
    • 'GCF_000025985.1'
    • 'GCF_000146045.2'
    • 'GCF_000151735.1'
    • 'GCF_000182965.3'
    • 'GCF_000195955.2'
    • 'GCF_000195995.1'
    • 'GCF_009914755.1'
    • 'GCF_020379485.1'

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 repeat feature is annotated; joins refseq.assembly_sequences.sequence_accession.
start INT 1-based inclusive start coordinate of the repeat feature interval on sequence_accession.
end INT 1-based inclusive end coordinate of the repeat feature interval on sequence_accession.
is_forward_strand BOOLEAN Whether the repeat feature interval is on the forward strand; null when the GFF strand is unspecified.
repeat_feature_id TEXT Local GFF3 ID of the repeat feature; not a stable RefSeq identifier.
repeat_type TEXT Source GFF3 repeat feature type.
annotation_method TEXT NCBI GFF column-2 annotation method or source, if supplied.
db_xrefs STRUCT(db TEXT, id TEXT)[] Database cross-references from GFF Dbxref; each item has a database and identifier, which may contain colons.
repeat_class TEXT Repeat classification from GFF rpt_type, if supplied, such as tandem, dispersed, or flanking.
repeat_family TEXT Repeat family from GFF rpt_family, if supplied.
repeat_unit_sequence TEXT Repeat unit sequence from GFF rpt_unit_seq, if supplied.
repeat_unit_range TEXT Source repeat unit range from GFF rpt_unit_range, if supplied.
satellite_type TEXT Satellite classification from GFF satellite, if supplied, such as microsatellite or minisatellite.
mobile_element_type TEXT Mobile element classification from GFF mobile_element_type, if supplied.
function TEXT Free text functional description from GFF function, if supplied.
experiments TEXT[] Percent-decoded experimental evidence entries from the comma-separated GFF experiment attribute.
is_partial BOOLEAN Whether NCBI marks the repeat feature as partial with GFF partial=true.
is_start_partial BOOLEAN Whether NCBI marks the column-4 start boundary as partial with a GFF start_range attribute.
is_end_partial BOOLEAN Whether NCBI marks the column-5 end boundary as partial with a GFF end_range attribute.
note TEXT Free text GFF Note annotation, if supplied.