NAME

Bio::Das::ProServer::SourceAdaptor::Transport::bioseqio - A ProServer transport module that works off any flat file that Bio::SeqIO supports.

VERSION

$Revision: 687 $

SYNOPSIS

DESCRIPTION

NB: This is *not* what you want to use if your files are large. As an example, a single query for "Z261_HUMAN" on the complete Swissprot file "sprot42.dat" takes several minutes.

SUBROUTINES/METHODS

init

query

DIAGNOSTICS

CONFIGURATION AND ENVIRONMENT

For sequential querying flat files, the following configuration entries are needed:

  filename      The name of the flat file to search.

  format        The format of the flat file.

If using Bio::DB::Flat (this is depedent on the existance of the 'index' configuration entry), the following additional configuration entries are needed:

  index       The type of index to create and/or use ('bdb' or
              'binarysearch').  Corresponds to the '-index'
              option of Bio::DB::Flat::new().

  dbname      The name of the database to create and/or
              use.  Corresponds to the '-dbname' option of
              Bio::DB::Flat::new().

  dbroot      The directory where the database index is
              or will be located.  Corresponds to the
              '-directory' option of Bio::DB::Flat::new().

DEPENDENCIES

INCOMPATIBILITIES

BUGS AND LIMITATIONS

AUTHOR

Andreas Kahari, andreas.kahari@ebi.ac.uk

LICENSE AND COPYRIGHT