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