skbio.sequence.RNA.translate_six_frames¶
-
RNA.
translate_six_frames
(genetic_code=1, *args, **kwargs)[source]¶ Translate RNA into protein using six possible reading frames.
State: Stable as of 0.4.0.
The six possible reading frames are:
1 (forward)
2 (forward)
3 (forward)
-1 (reverse)
-2 (reverse)
-3 (reverse)
Translated sequences are yielded in this order.
- Parameters
genetic_code (int, GeneticCode, optional) – Genetic code to use in translation. If
int
, used as a table ID to look up the corresponding NCBI genetic code.args (tuple) – Positional arguments accepted by
GeneticCode.translate_six_frames
.kwargs (dict) – Keyword arguments accepted by
GeneticCode.translate_six_frames
.
- Yields
Protein – Translated sequence in the current reading frame.
Notes
This method is faster than (and equivalent to) performing six independent translations using, for example:
(seq.translate(reading_frame=rf) for rf in GeneticCode.reading_frames)
RNA sequence’s metadata are included in each translated protein sequence. Positional metadata are not included.
Examples
Translate RNA into protein using the six possible reading frames and NCBI’s standard genetic code (table ID 1, the default genetic code in scikit-bio):
>>> from skbio import RNA >>> rna = RNA('AUGCCACUUUAA') >>> for protein in rna.translate_six_frames(): ... protein ... print('') Protein -------------------------- Stats: length: 4 has gaps: False has degenerates: False has definites: True has stops: True -------------------------- 0 MPL* Protein -------------------------- Stats: length: 3 has gaps: False has degenerates: False has definites: True has stops: False -------------------------- 0 CHF Protein -------------------------- Stats: length: 3 has gaps: False has degenerates: False has definites: True has stops: False -------------------------- 0 ATL Protein -------------------------- Stats: length: 4 has gaps: False has degenerates: False has definites: True has stops: False -------------------------- 0 LKWH Protein -------------------------- Stats: length: 3 has gaps: False has degenerates: False has definites: True has stops: True -------------------------- 0 *SG Protein -------------------------- Stats: length: 3 has gaps: False has degenerates: False has definites: True has stops: False -------------------------- 0 KVA