ncbi_taxonomy.genetic_codes

Python

In [1]:

import bedrock_bio as bb

rel = bb.load_table('ncbi_taxonomy.genetic_codes')

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

Out[1]:

	sources	genetic_code_id	abbreviation	name	amino_acid_translation	start_codon_table
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	0	None	Unspecified	...	...
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	1	None	Standard	FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSS...	---M------**--*----M---------------M----------...
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	10	None	Euplotid Nuclear	FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSS...	----------**-----------------------M----------...
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	11	None	Bacterial, Archaeal and Plant Plastid	FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSS...	---M------**--*----M------------MMMM----------...
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	12	None	Alternative Yeast Nuclear	FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSS...	----------**--*----M---------------M----------...

R

In [1]:

library(bedrockbio)

lf <- load_table("ncbi_taxonomy.genetic_codes")
df <- head(lf, 5) |> collect()

head(df)

Out[1]:

Sample output (5 rows, showing 5 of 6 columns)
   genetic_code_id | abbreviation | name                     | amino_acid_translation   | start_codon_table
   --------------- | ------------ | ------------------------ | ------------------------ | ------------------------
0  0               | —            | Unspecified              |                          |
1  1               | —            | Standard                 | FFLLSSSSYY**CC*WLLLLPPP… | ---M------**--*----M---…
2  10              | —            | Euplotid Nuclear         | FFLLSSSSYY**CCCWLLLLPPP… | ----------**-----------…
3  11              | —            | Bacterial, Archaeal and… | FFLLSSSSYY**CC*WLLLLPPP… | ---M------**--*----M---…
4  12              | —            | Alternative Yeast Nucle… | FFLLSSSSYY**CC*WLLLSPPP… | ----------**--*----M---…

Description

NCBI genetic code definitions used by taxonomy nodes, one row per genetic code.

Partitions

Not partitioned.

Schema

Column	Type	Description
sources	STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]	Source provenance for the row.
genetic_code_id	TEXT	NCBI genetic code ID.
abbreviation	TEXT	NCBI genetic code abbreviation, if supplied.
name	TEXT	NCBI genetic code name.
amino_acid_translation	TEXT	NCBI translation table character string that maps codons to amino acids.
start_codon_table	TEXT	NCBI start codon character string aligned to amino_acid_translation.