DATABASE.md

###Imports

from BioSQL import BioSeqDatabase
from Bio import SeqIO
from Bio import Entrez
from toolz import compose

Getting databse handle

server = BioSeqDatabase.open_database(driver="sqlite3",db="biodatabase")
dengue = server.open_database("Dengue")
db = server.new_database("Influenza", description="Just for testing")
In[]: db.adaptor.list_biodatabase_names()
out[] ['Dengue', 'Influenza']

###Queries queries can be done manually, from a number of different tables.

sql = compose(list, db.adaptor.cursor.execute)
sql('SELECT * FROM bioentry') # basic info accession, desc.
sql(r"select term_id from term where name='source'")

or via the lookup method:

db.lookup(accession='EU569704')

Valid lookup kwargs:

display_id
name
accession
primary_id
version
gi

also:

def get_all_records(db):
    return map(db.__getitem__, db.get_all_primary_ids())

Get All countries/locations:

In[206]: sql(r"""SELECT * FROM seqfeature_qualifier_value WHERE term_id =
    (select term_id from term where name='country')""")

Out[206]: [(1, 15, 1, u'USA: Puerto Rico')]

from the SeqRecord object, usually the first feature, and usually of type source:

In[]: source = filter(lambda x: x.type == 'source', rec.features)
In[]: source[0].qualifiers['country']
Out[]: 'USA: Puerto Rico'

###RegEx search sqlite does not have regex search by default so have to register the function

import re
def re_fn(expr, item):
    reg = re.compile(expr, re.I)
    return reg.search(item) is not None
db.adaptor.conn.create_function("REGEXP", 2, re_fn)

# works now
sql(r"select * from seqfeature_qualifier_value where  value REGEXP '.*' ")

sql(r"select value from seqfeature_qualifier_value where value REGEXP '.*USA.*'")
# USA: Puerto Rico

###Inserting Records

Entrez.email = "[email protected]"
handle = Entrez.efetch(db="nuccore", id="EU569704", rettype="gb", retmode="text") #id=accession
count = db.load(SeqIO.parse(handle, "genbank"))
server.commit()

Other Stuff

map schema for where those features are and the like Tables: seqfeature, location, comment, etc.