[Biopython] Integrating SQL query to biopython

[Brad Chapman]

Animesh;

> I am running small SQL queries to select sequences from a local BIOSQL
> database. One instance such query is as follows:
>
> SELECT  biosequence.*
> FROM    biosequence JOIN bioentry USING (bioentry_id)
> WHERE   biosequence.seq NOT LIKE "%X%"
> AND   biosequence.alphabet = 'protein' 
>
> I am wondering, how do I integrate this SQL query with Biopython code to get
> the output in form of SeqRecord or Seq objects.

If you have the interval bioentry IDs you can use the BioSQL code
directly to get SeqRecord compatible objects:

from BioSQL import BioSeqDatabase
from BioSQL.BioSeq import DBSeqRecord

server = BioSeqDatabase.open_database(driver="MySQLdb", user="root",
                     passwd = "", host = "localhost", db="bioseqdb")
rec = DBSeqRecord(server.adaptor, your_bioentry_id)

Hope this helps,
Brad