Bio::Das::ProServer::SourceAdaptor::Transport::bioseqio - A ProServer transport module that works off any flat file that Bio::SeqIO supports.
$Revision: 687 $
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.
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().
Andreas Kahari, andreas.kahari@ebi.ac.uk
To install Bio::Das::ProServer, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Das::ProServer
CPAN shell
perl -MCPAN -e shell install Bio::Das::ProServer
For more information on module installation, please visit the detailed CPAN module installation guide.