old_contents: #!/usr/bin/env python
  import sys
  from getpass import getpass
  from BioSQL import BioSeqDatabase
  from common import standard_options, generate_placeholders, chunks, extract_feature_sql
  
  def get_seqfeature_for_db(server, biodb):
      ''' find all seqfeatures that have the given value for the qualifier
          returns a list of seqfeature_id
      '''
      sql = "SELECT qv.seqfeature_id FROM seqfeature_qualifier_value qv join seqfeature s using(seqfeature_id) join bioentry b using(bioentry_id) join biodatabase bd using(biodatabase_id) WHERE bd.name = %s"
      return server.adaptor.execute_and_fetchall(sql, (biodb,))
  
  def main(args):
      server = BioSeqDatabase.open_database(driver=args.driver, db=args.database, user=args.user, host=args.host, passwd=args.password)
  
      if args.output_format == 'fasta':
          from Bio import SeqIO
          db = server[args.database_name]
          for rec in db.values():
              SeqIO.write(rec, sys.stdout, args.output_format)
      else:
  
          seqfeature_ids = get_seqfeature_for_db(server, args.database_name)
  
          if args.output_format == 'feat-prot':
              extract_feature_sql(server, seqfeature_ids, type=['CDS'], translate=True )
          elif args.output_format == 'feat-nucl':
              extract_feature_sql(server, seqfeature_ids )
  
  
  if __name__ == "__main__":
      parser = standard_options()
      parser.add_argument('-D', '--database-name', help='namespace of the database that you want to add into', dest='database_name', required=True)
      parser.add_argument('-o', '--output_format', help='output format of the selected sequences', choices=['feat-prot', 'feat-nucl', 'fasta'], default='feat-prot')
      args = parser.parse_args()
      if args.password is None:
          args.password = getpass("Please enter the password for user " + \
                  args.user + " on database " + args.database)
      main(args)
  
  
new_contents: #!/usr/bin/env python
  import sys
  from getpass import getpass
  from BioSQL import BioSeqDatabase
  from common import standard_options, generate_placeholders, chunks, extract_feature_sql
  
  def get_seqfeature_for_db(server, biodb):
      ''' find all seqfeatures that have the given value for the qualifier
          returns a list of seqfeature_id
      '''
      sql = "SELECT qv.seqfeature_id FROM seqfeature_qualifier_value qv join seqfeature s using(seqfeature_id) join bioentry b using(bioentry_id) join biodatabase bd using(biodatabase_id) WHERE bd.name = %s"
      return server.adaptor.execute_and_fetchall(sql, (biodb,))
  
  def main(args):
      server = BioSeqDatabase.open_database(driver=args.driver, db=args.database, user=args.user, host=args.host, passwd=args.password)
  
      if args.output_format == 'fasta':
          from Bio import SeqIO
          db = server[args.database_name]
          for rec in db.values():
              SeqIO.write(rec, sys.stdout, args.output_format)
      else:
  
          seqfeature_ids = get_seqfeature_for_db(server, args.database_name)
  
          if args.output_format == 'feat-prot':
              extract_feature_sql(server, seqfeature_ids, type=['CDS'], translate=True )
          elif args.output_format == 'feat-nucl':
              extract_feature_sql(server, seqfeature_ids )
  
  
  if __name__ == "__main__":
      parser = standard_options()
      parser.add_argument('-D', '--database-name', help='namespace of the database that you want to output genes from', dest='database_name', required=True)
      parser.add_argument('-o', '--output_format', help='output format of the selected sequences', choices=['feat-prot', 'feat-nucl', 'fasta'], default='feat-prot')
      args = parser.parse_args()
      if args.password is None:
          args.password = getpass("Please enter the password for user " + \
                  args.user + " on database " + args.database)
      main(args)
  
  
subject: change help message for -D option