[Biopython] Is this a valid genbank record?

[Peter Cock]

On Wed, Jan 18, 2012 at 4:31 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> On Jan 18, 2012, at 9:34 AM, Peter Cock wrote:
>> Any idea why this example is:
>>
>> join(bond(127),bond(127),bond(130),bond(130),bond(138),
>> bond(138),bond(139),bond(138))
>>
>> rather than:
>>
>> bond(127,127,130,130,138,138,139,138)
>>
>> or indeed by so many of the residues are bonded more than
>> once?
>>
>> Peter
>
> No, that one is particularly odd, but there isn't a reason I could
> see where this couldn't be supported, it's just a join of simple locations.
> Seems this is something that may be auto-generated, wouldn't be
> surprised to see more of these.
>
> As to whether it's a valid GenBank record, well, considering the source
> of the record is NCBI, I think it's safe to say it's valid.
>
> (though again, this all comes back to how helpful it would be to have
> documentation re: how bond() is defined within the context of the
> feature table)

There is precedent for the NCBI publishing GenBank files which
didn't conform to the published specification - but in the absence
of any spec we're basically stuck with guessing what they intend.
I will attempt to enquirer...

Peter