API Reference

This section contains a complete reference of the pyaragorn module API.

Module

Bindings to ARAGORN, a (t|mt|tm)RNA gene finder.

pyaragorn.ARAGORN_VERSION

The version of ARAGORN currently wrapped in PyARAGORN.

Type:

str

pyaragorn.TRANSLATION_TABLES

A set containing all the translation tables supported by PyARAGORN.

Type:

set of int

Example

PyARAGORN can work on any DNA sequence stored in either a text or a byte array. To load a sequence from one of the common sequence formats, you can use an external dedicated library such as Biopython:

>>> import gzip
>>> import Bio.SeqIO
>>> with gzip.open("CP001621.fna.gz", "rt") as f:
...     record = Bio.SeqIO.read(f, "fasta")

Then use PyARAGORN to find the tRNA genes using the bacterial genetic code (translation table 11):

>>> import pyaragorn
>>> rna_finder = pyaragorn.RNAFinder(11, trna=True, tmrna=False)
>>> for gene in rna_finder.find_rna(record.seq.encode()):
...     print(gene.anticodon, gene.amino_acid, gene.begin, gene.end)
tag Leu 87124 87207
ttt Lys 87210 87285
...

The gene coordinates are 1-indexed, inclusive, similarly to Pyrodigal genes.

References

• Laslett, Dean, and Björn Canback. “ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.” Nucleic acids research vol. 32,1 11-6. 2 Jan. 2004, doi:10.1093/nar/gkh152. PMID:14704338. :pmcid:`PMC373265`.

• Laslett, Dean, and Björn Canbäck. “ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences.” Bioinformatics (Oxford, England) vol. 24,2 (2008): 172-5. doi:10.1093/bioinformatics/btm573. PMID:18033792.

RNA Finder

RNAFinder

A configurable RNA gene finder.

Genes

Gene	A gene identified by ARAGORN.
TRNAGene	A transfer RNA (tRNA) gene.
TMRNAGene	A transfer-messenger RNA (tmRNA) gene.