[Biopython-dev] A modification to BioSQL

[Brian Osborne]

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
> 
> 
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev