RNAFinder

class pyaragorn.RNAFinder

A configurable RNA gene finder.

__init__(translation_table=1, *, trna=True, tmrna=True, linear=False, threshold_scale=1.0)

Create a new RNA finder.

Parameters:

translation_table (int, optional) – The translation table to use. Check the List of genetic codes page listing all genetic codes for the available values, or the pyaragorn.TRANSLATION_TABLES constant for allowed values.

Keyword Arguments:

• trna (bool) – Enable detection of tRNA genes. Set to False to disable.

• trmna (bool) – Enable detection of tmRNA genes. Set to False to disable.

• linear (bool) – Set to True to assume that the given sequences have linear topology (no closed genomes).

• threshold_scale (float, optional) – Rescale scoring thresholds from the default levels. Defaults to 1.0 (no rescaling). Set to e.g. 0.95 to report possible pseudogenes by lowering the threshold by 5%.

Added in version 0.3.0: The threshold_scale keyword argument.

find_rna(sequence)

Find RNA genes in the input DNA sequence.

Parameters:

sequence (str or buffer) – The nucleotide sequence to process, either as a string of nucleotides (upper- or lowercase), or as an object implementing the buffer protocol.

Returns:

list of Gene – A list of Gene (either TRNAGene or TMRNAGene) corresponding to RNA genes detected in the sequence according to the RNAFinder parameters.

linear

Whether input sequences are assumed to have linear topology.

Type:

bool

threshold_scale

The scale used to change the default thresholds.

Added in version 0.3.0.

Type:

float

tmrna

Whether tmRNA detection is enabled.

Type:

bool

translation_table

The translation table in use by this object.

Type:

int

trna

Whether tRNA detection is enabled.

Type:

bool