"""Example of registering a BioSQL database using Biopython-specific system.
"""
# register our BioSQL database
from Bio.sources import BioSQL
fred_db = BioSQL(name = "fred",
doc = "Test MySQL server on fred",
db_host = "192.168.0.192",
db_user = "******",
db_passwd = "",
sql_db = "test_biosql",
namespace_db = "embl_rod")
from Bio import register_db
register_db(name = "biosql-embl-fred",
key = "accession",
source = fred_db,
failure = [])
# deal with the database
from Bio import db
biosql_db = db["biosql-embl-fred"]
rec = biosql_db["AB030760"]
print rec
print rec.description
print rec.id
print rec.name
print rec.seq.data[0:20]
"""Example of registering an Indexed file using the Biopython system.
"""
# register our indexed file
from Bio.sources import IndexedFile
index_file = IndexedFile(name = "test",
doc = "Test indexed file",
dbname = "/home/chapmanb/bioppjx/tmp/test")
from Bio import register_db
register_db(name = "indexfile-test-swissprot",
key = "id",
source = index_file,
failure = [])
# deal with the database
from Bio import db
indexed_db = db["indexfile-test-swissprot"]
rec = indexed_db["N33_HUMAN"]
print rec
print rec.description
print rec.id
print rec.name
print rec.seq.data[0:20]
"""Example of registering a BioCorba database using Biopython-specific system.
"""
# register our BioCorba database
from Bio.sources import BioCorba
fred_corba = BioCorba(name = "fred",
doc = "Test CORBA server on fred",
ior_ref = "http://fred/CORBA/py_collection.ior")
from Bio import register_db
register_db(name = "biocorba-test-fred",
key = "accession",
source = fred_corba,
failure = [])
# deal with the database
from Bio import db
biocorba_db = db["biocorba-test-fred"]
rec = biocorba_db["X55053"]
print rec
print rec.description
print rec.id
print rec.name
print rec.seq.data[0:20]
"""Example of registering a database with the Biopython-specific system.
"""
from Bio.sources import CGI
local_cgi = CGI(name = "local_cgi",
delay = 0.0,
cgi = "http://www.myserver.org/cgi-bin/my_local.cgi",
url = "http://www.myserver.org/cgi_documentation.html",
doc = "Query a local databases",
failure_cases = [])
import Martel
my_failures = [
(Martel.Str("Sequence not available"), "No sequence found")]
from Bio import register_db
register_db(name = "nucleotide-genbank-local",
key = "uid",
source = local_cgi,
failure = my_failures)
register_db(name = "genbank", behavior = "concurrent")
from Bio import group_db
group_db("genbank", "nucleotide-genbank-local")
group_db("genbank", "nucleotide-genbank-cgi")
from Bio import db
print db.keys()
