[Biopython-dev] [Bug 2381] translate and transcibe methods for the Seq object (in Bio.Seq)

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http://bugzilla.open-bio.org/show_bug.cgi?id=2381





------- Comment #36 from bsouthey at gmail.com  2008-11-05 15:30 EST -------
(In reply to comment #35)
Okay, this is what I think of the main uses for translation. All these can be
easily achieved by the translate arguments table='Standard' and stop_symbol='*'
with very little code. So I do not see any need for any extra arguments except
for convenience. (I have these uses in file that I will upload after this.)

So really my only issue left is what is the expected behaviour for:
a) to_stop_codon=True if there are no valid stop codons (my understanding of
to_stop). 
b) from_start_codon=True (or init=True etc) if there are no valid start codons


1) Translation in some given forward frame - reverse frames should be obvious.
Looping over these will give all three frames but that could return multiple
Seq objects.

2) Translation between any range of locations. From Peter's example, extracting
the region between 5234 to 5530 in the complete sequence will give the yaaX
gene CDS that can be translated into the protein sequence.

3a) Translate to the first valid stop codon. Perhaps not as expected because it
should respect the frame so try:
3b) Translate to the first valid stop codon with respect to selected frame.
3c) Alternatively use to_stop=True argument of the translate. Here translation
is to the first valid stop codon OR the end of the sequence. This second aspect
is not documented.

4a) Start translation at first start codon. Again, does not respect frame so
try:
4b) Translate to the first valid start codon with respect to selected frame.

In both cases of 4) the very first codon must be checked against the defined
start_codon list in the appropriate CodonTable.

Obviously 3) and 4) should raise exceptions if stop or start codons are not
found because of the specific request to stop or start translation. But, as in
3c), this could be relaxed to include the end of the sequence. I am not sure
the behaviour if there is no valid start codon.

Also some variation of 3a) and 4a) could be used to find possible open reading
frames (from a start codon to stop codon). But this could return more than one
Seq object. 


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