[Biopython-dev] A modification to BioSQL

[Peter Cock]

Thanks Brian,

OK, good. Now since you also seem familiar with the
BioPerl/BioSQL setup, does it also look for a special
qualifier "source" in the same way?

i.e. Is this equivalent to the BioPerl source_tag() method.
mentioned earlier?

(You could probably test this with a hand edited GenBank
file adding a "source" qualifier to a pre-existant feature
then loading it into BioSQL with BioPerl - I don't think I
have a suitable test setup up and running the moment
to try that myself.)

If so, then I'll look at getting the PR updated, tested,
and merged in.

Peter

On Wed, Jun 24, 2015 at 4:58 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
> Peter,
>
> Tested the ctSkennerton code, it does what you’d expect. When a SeqRecord is loaded with a feature like this:
>
> feat = SeqFeature(loc, qualifiers={"host": "human"}, type="test_domain")
>
> the SeqFeature in the database has the default “source_term” of 'EMBL/GenBank/SwissProt’.
>
> But this:
>
> feat = SeqFeature(loc, qualifiers={"source": "NCBI", "host": "human"}, type="test_domain”)
>
> sets the source_term to “NCBI”.
>
> Thanks again,
>
> Brian O.
>
>> On Jun 23, 2015, at 9:49 AM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>
>> Peter,
>>
>> Yes, will test.
>>
>> Thanks once again.
>>
>> BIO
>>
>>
>>> On Jun 23, 2015, at 9:41 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>>
>>> On Tue, Jun 23, 2015 at 2:34 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>>> Peter,
>>>>
>>>> So that code submitted by ctSkennerton would certainly work for me as well.
>>>> Looks like you had no problem with the change, can the merge conflict be
>>>> resolved?
>>>>
>>>> Thanks again,
>>>>
>>>> Brian O.
>>>
>>> I'm not sure what's up with TravisCI and a possible merge conflict.
>>> Any conflict is likely just cosmetic.
>>>
>>> Could you try testing if ctSkennerton's branch works for you?
>>>
>>> (You'd need to know basic git, and be able to install Biopython
>>> from source - fairly easy under Linux or Mac OS X)
>>>
>>> Peter
>>
>>
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>