[Biopython-dev] A modification to BioSQL

[Brian Osborne]

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.


> On Jun 22, 2015, at 5:22 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
> 
> Peter,
> 
> Interesting exchange, was not aware of it.
> 
> Yes, in BioPerl there’s a source_tag() method.
> 
> Thanks again,
> 
> Brian O.
> 
>> On Jun 22, 2015, at 4:44 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> 
>> Hi Brian,
>> 
>> Are you familiar with the logic BioPerl uses to set this field?
>> See also https://github.com/biopython/biopython/pull/366
>> 
>> Peter
>> 
>> On Mon, Jun 22, 2015 at 9:11 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>> All,
>>> 
>>> I’ve been using the BioSQL schema with Bioperl and would like to start doing
>>> the same with Biopython, but there’s a limitation I’d like to fix. Here’s
>>> the relevant table in the BioSQL schema, seqfeature:
>>> 
>>>    Column     |         Type          |                        Modifiers
>>> | Storage  | Stats target | Description
>>> ----------------+-----------------------+---------------------------------------------------------+----------+--------------+-------------
>>> seqfeature_id  | integer               | not null default
>>> nextval('seqfeature_pk_seq'::regclass) | plain    |              |
>>> bioentry_id    | integer               | not null
>>> | plain    |              |
>>> type_term_id   | integer               | not null
>>> | plain    |              |
>>> source_term_id | integer               | not null
>>> | plain    |              |
>>> display_name   | character varying(64) |
>>> | extended |              |
>>> rank           | integer               | not null default 0
>>> | plain    |              |
>>> 
>>> Note that required field, source_term_id. In the work I’ve been doing with
>>> Bioperl I’ve been setting this “source term” to different values (e.g.
>>> “NCBI”) depending on where the tag/value data in the feature comes from.
>>> 
>>> But here’s the code that makes a persistent feature, from BioSQL/Loader.py:
>>> 
>>>   def _load_seqfeature_basic(self, feature_type, feature_rank,
>>> bioentry_id):
>>>       """Load the first tables of a seqfeature and returns the id
>>> (PRIVATE).
>>> 
>>>       This loads the "key" of the seqfeature (ie. CDS, gene) and
>>>       the basic seqfeature table itself.
>>>       """
>>>       ontology_id = self._get_ontology_id('SeqFeature Keys')
>>>       seqfeature_key_id = self._get_term_id(feature_type,
>>>                                             ontology_id=ontology_id)
>>>       # XXX source is always EMBL/GenBank/SwissProt here; it should depend
>>> on
>>>       # the record (how?)
>>>       source_cat_id = self._get_ontology_id('SeqFeature Sources')
>>>       source_term_id = self._get_term_id('EMBL/GenBank/SwissProt',
>>>                                          ontology_id=source_cat_id)
>>> 
>>>       sql = r"INSERT INTO seqfeature (bioentry_id, type_term_id, " \
>>>             r"source_term_id, rank) VALUES (%s, %s, %s, %s)"
>>>       self.adaptor.execute(sql, (bioentry_id, seqfeature_key_id,
>>>                                  source_term_id, feature_rank + 1))
>>>       seqfeature_id = self.adaptor.last_id('seqfeature')
>>> 
>>>       return seqfeature_id
>>> 
>>> This code always sets the source term to “ EMBL/GenBank/SwissProt”, and it
>>> can not be set to anything else. A better idea is to have a method to set
>>> and get this, e.g. source(), just as you can set the “type” of the feature.
>>> The way to do this is to subclass SeqFeature to make DBSeqFeature, just as
>>> Seq is subclassed to make DBSeq and SeqRecord is subclassed to make
>>> DBSeqRecord in BioSQL/Seq.py.
>>> 
>>> So I propose to fork, code, and send a pull request for this. What do you
>>> think?
>>> 
>>> Thanks again,
>>> 
>>> Brian O.
>>> 
>>> _______________________________________________
>>> Biopython-dev mailing list
>>> Biopython-dev at mailman.open-bio.org
>>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
> 
> 
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