Roger Pettett > Bio-Das-ProServer > Bio::Das::ProServer::SourceAdaptor::Transport::bioseqio

Download:
Bio-Das-ProServer-2.20.tar.gz

Dependencies

Annotate this POD

CPAN RT

Open  0
View/Report Bugs
Module Version: 687   Source  

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 ^

syntax highlighting: