BioSQL package

Submodules

• BioSQL.BioSeq module
  • DBSeqRecord
    • DBSeqRecord.__init__()
    • DBSeqRecord.seq
    • DBSeqRecord.dbxrefs
    • DBSeqRecord.features
    • DBSeqRecord.annotations
• BioSQL.BioSeqDatabase module
  • open_database()
  • DBServer
    • DBServer.__init__()
    • DBServer.__repr__()
    • DBServer.__getitem__()
    • DBServer.__len__()
    • DBServer.__contains__()
    • DBServer.__iter__()
    • DBServer.keys()
    • DBServer.values()
    • DBServer.items()
    • DBServer.__delitem__()
    • DBServer.new_database()
    • DBServer.load_database_sql()
    • DBServer.commit()
    • DBServer.rollback()
    • DBServer.close()
  • Adaptor
    • Adaptor.__init__()
    • Adaptor.last_id()
    • Adaptor.autocommit()
    • Adaptor.commit()
    • Adaptor.rollback()
    • Adaptor.close()
    • Adaptor.fetch_dbid_by_dbname()
    • Adaptor.fetch_seqid_by_display_id()
    • Adaptor.fetch_seqid_by_accession()
    • Adaptor.fetch_seqids_by_accession()
    • Adaptor.fetch_seqid_by_version()
    • Adaptor.fetch_seqid_by_identifier()
    • Adaptor.list_biodatabase_names()
    • Adaptor.list_bioentry_ids()
    • Adaptor.list_bioentry_display_ids()
    • Adaptor.list_any_ids()
    • Adaptor.execute_one()
    • Adaptor.execute()
    • Adaptor.executemany()
    • Adaptor.get_subseq_as_string()
    • Adaptor.execute_and_fetch_col0()
    • Adaptor.execute_and_fetchall()
  • MysqlConnectorAdaptor
    • MysqlConnectorAdaptor.execute_one()
    • MysqlConnectorAdaptor.execute_and_fetch_col0()
    • MysqlConnectorAdaptor.execute_and_fetchall()
  • BioSeqDatabase
    • BioSeqDatabase.__init__()
    • BioSeqDatabase.__repr__()
    • BioSeqDatabase.get_Seq_by_id()
    • BioSeqDatabase.get_Seq_by_acc()
    • BioSeqDatabase.get_Seq_by_ver()
    • BioSeqDatabase.get_Seqs_by_acc()
    • BioSeqDatabase.__getitem__()
    • BioSeqDatabase.__delitem__()
    • BioSeqDatabase.__len__()
    • BioSeqDatabase.__contains__()
    • BioSeqDatabase.__iter__()
    • BioSeqDatabase.keys()
    • BioSeqDatabase.values()
    • BioSeqDatabase.items()
    • BioSeqDatabase.lookup()
    • BioSeqDatabase.load()
• BioSQL.DBUtils module
  • Generic_dbutils
    • Generic_dbutils.__init__()
    • Generic_dbutils.tname()
    • Generic_dbutils.last_id()
    • Generic_dbutils.execute()
    • Generic_dbutils.executemany()
    • Generic_dbutils.autocommit()
  • Sqlite_dbutils
    • Sqlite_dbutils.execute()
    • Sqlite_dbutils.executemany()
  • Mysql_dbutils
    • Mysql_dbutils.last_id()
  • Psycopg2_dbutils
    • Psycopg2_dbutils.autocommit()
  • Pgdb_dbutils
    • Pgdb_dbutils.autocommit()
  • get_dbutils()
• BioSQL.Loader module
  • DatabaseLoader
    • DatabaseLoader.__init__()
    • DatabaseLoader.load_seqrecord()
  • DatabaseRemover
    • DatabaseRemover.__init__()
    • DatabaseRemover.remove()

Module contents

Storing and retrieve biological sequences in a BioSQL relational database.

See:

• http://biopython.org/wiki/BioSQL

• http://www.biosql.org/