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.
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
.
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