refseq.cds

Python

In [1]:

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()

Out[1]:

	sources	assembly_accession	sequence_accession	start	end	is_forward_strand	phase	cds_id	parent_id	annotation_method	...	product	protein_accession	translation_table	translation_exceptions	part	is_partial	is_start_partial	is_end_partial	exception	note
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes...	GCF_000001215.4	NC_004353.4	930	1079	True	0	cds-NP_001104092.2	rna-NM_001110622.3	RefSeq	...	JYalpha	NP_001104092.2	<NA>	[]	<NA>	False	False	False	None	None
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes...	GCF_000001215.4	NC_004353.4	1144	1410	True	0	cds-NP_001104092.2	rna-NM_001110622.3	RefSeq	...	JYalpha	NP_001104092.2	<NA>	[]	<NA>	False	False	False	None	None
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes...	GCF_000001215.4	NC_004353.4	1768	3851	True	0	cds-NP_001104092.2	rna-NM_001110622.3	RefSeq	...	JYalpha	NP_001104092.2	<NA>	[]	<NA>	False	False	False	None	None
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes...	GCF_000001215.4	NC_004353.4	4353	4527	True	1	cds-NP_001104092.2	rna-NM_001110622.3	RefSeq	...	JYalpha	NP_001104092.2	<NA>	[]	<NA>	False	False	False	None	None
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes...	GCF_000001215.4	NC_004353.4	4592	4824	True	0	cds-NP_001104092.2	rna-NM_001110622.3	RefSeq	...	JYalpha	NP_001104092.2	<NA>	[]	<NA>	False	False	False	None	None

R

In [1]:

library(bedrockbio)
library(dplyr)

lf <- load_table("refseq.cds")
df <- filter(lf, assembly_accession == "GCF_000001215.4") |> collect()

head(df)

Out[1]:

Sample output (5 rows, showing 8 of 21 columns)
   assembly_accession | sequence_accession | start | end  | is_forward_strand | phase | cds_id             | parent_id
   ------------------ | ------------------ | ----- | ---- | ----------------- | ----- | ------------------ | ------------------
0  GCF_000001215.4    | NC_004353.4        | 930   | 1079 | true              | 0     | cds-NP_001104092.2 | rna-NM_001110622.3
1  GCF_000001215.4    | NC_004353.4        | 1144  | 1410 | true              | 0     | cds-NP_001104092.2 | rna-NM_001110622.3
2  GCF_000001215.4    | NC_004353.4        | 1768  | 3851 | true              | 0     | cds-NP_001104092.2 | rna-NM_001110622.3
3  GCF_000001215.4    | NC_004353.4        | 4353  | 4527 | true              | 1     | cds-NP_001104092.2 | rna-NM_001110622.3
4  GCF_000001215.4    | NC_004353.4        | 4592  | 4824 | true              | 0     | cds-NP_001104092.2 | rna-NM_001110622.3

Description

RefSeq coding sequence (CDS) intervals.

One row represents one CDS interval; a multi-interval CDS repeats its local cds_id across rows.

parent_id is the local ID of the immediate parent feature.

It is usually a transcript ID, but can be a gene ID when no transcript feature is annotated. translation_exceptions retains qualifiers needed to interpret exceptional coding translation.

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_000002285.3'
  • '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_011100685.1'
  • '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

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 CDS interval is annotated; joins refseq.assembly_sequences.sequence_accession.
start	INT	1-based inclusive start coordinate of the CDS interval on sequence_accession.
end	INT	1-based inclusive end coordinate of the CDS interval on sequence_accession.
is_forward_strand	BOOLEAN	Whether the CDS interval is on the forward strand; null when the GFF strand is unspecified.
phase	Int8	GFF CDS reading frame offset—the number of bases at the coding direction start of this interval before the next complete codon (0, 1, or 2).
cds_id	TEXT	Local GFF3 ID of the CDS feature; not a stable RefSeq identifier and shared by its intervals.
parent_id	TEXT	Local GFF3 Parent ID of the immediate parent feature; usually a transcript ID but sometimes a gene ID.
annotation_method	TEXT	NCBI GFF column-2 annotation method or source, such as BestRefSeq, Gnomon, or GeneMarkS+, 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.
product	TEXT	Protein product name from the GFF product attribute, if supplied.
protein_accession	TEXT	Versioned RefSeq or INSDC protein accession from the GFF protein_id attribute, if supplied.
translation_table	Int8	NCBI genetic code table number from GFF transl_table, if supplied.
translation_exceptions	TEXT[]	Percent-decoded CDS translation exception expressions from the comma-separated GFF transl_except attribute.
part	INT	Ordinal interval number from the GFF part=N or part=N/M attribute, if supplied.
is_partial	BOOLEAN	Whether NCBI marks the CDS 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.
exception	TEXT	NCBI GFF exception annotation describing a transcriptional or translational exception, if supplied.
note	TEXT	Free text GFF Note annotation, if supplied.