"""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()