[Biopython] Is this a valid genbank record?

[Peter Cock]

On Wed, Jan 18, 2012 at 3:24 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> On Jan 18, 2012, at 8:50 AM, Peter Cock wrote:
>
>> On Wed, Jan 18, 2012 at 11:11 AM, Michael Thon <mike.thon at gmail.com> wrote:
>>>
>>> On Jan 18, 2012, at 12:03 PM, Peter Cock wrote:
>>>
>>>> On Wed, Jan 18, 2012 at 10:14 AM, Michael Thon <mike.thon at gmail.com> wrote:
>>>>>  They have weird feature locations:
>>>>>
>>>>>     Het             join(bond(127),bond(127),bond(130),bond(130),bond(138),
>>>>>                     bond(138),bond(139),bond(138))
>>>>>
>>
>> Do you actually need to do anything with this feature? If not, then
>> the pragmatic solution is we issue a warning but otherwise ignore
>> the feature and continue parsing. I'm struggling to grok exactly
>> what this location is trying to convey - maybe I should read the
>> associated paper?
>
> GenPept is littered with these.  With bioperl we only attempt to
> support 'bond' types for round-tripping, but I don't recall whether
> this has been extensively tested, though it would be easy enough
> to add this in to see if the location factory will handle this properly
> (both to and from a location string).
>
> Do wish NCBI would document this more...

+1

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