br_biofetch(1) [debian man page]

BIORUBY(1)						      General Commands Manual							BIORUBY(1)

NAME

       br_biofetch.rb -- biofetch client

SYNOPSIS

       br_biofetch.rb [-s server]  [db]  [id]  [style]	[format]

DESCRIPTION

       This manual page documents briefly the br_biofetch.rb.

       br_biofetch.rb  is  a  very  simple  biofetch client. You can connect to a biofetch server and retrieve database entries including sequence
       information.

OPTIONS

       -s	 Specify the URL of the BioFetch CGI (default is http://bioruby.org/cgi-bin/biofetch.rb)

       -e	 Use the EBI server at http://www.ebi.ac.uk/cgi-bin/dbfetch

       -r	 Use the BioRuby server at http://bioruby.org/cgi-bin/biofetch.rb

       db	 Database name. This includes options like refseq, genbank, embl, swissprot, etc. This option depends on which biofetch server you
		 are using.

       id	 entry id

       style	 'raw' or 'html' (default is 'raw')

       format	 Output format ('default, 'fasta', 'etc')

SEE ALSO

       bar (1), baz (1).

AUTHOR

       This manual page was written by David Nusinow dnusinow@debian.org for the Debian system (but may be used by others).  Permission is granted
       to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by
       the Free Software Foundation.

       On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

																	BIORUBY(1)

BIORUBY(1)						      General Commands Manual							BIORUBY(1)

NAME

       br_bioflat.rb -- OBDA flat file indexer

SYNOPSIS

       Search:

       br_bioflat.rb [--search]  [options...]

       br_bioflat.rb [--search]  [--location DIR]  [--dbname DBNAME]  [options...]  [KEYWORDS]

       Create index:

       br_bioflat.rb [--create]  [--location DIR]  [--dbname DBNAME]  [--format genbank|embl|fasta]  [options...]  [--files FILES...]

       Update index:

       br_bioflat.rb [--update]  [--location DIR]  [--dbname DBNAME]  [options...]  [--files FILES...]

       Show namespaces:

       br_bioflat.rb [--show-namespaces]  [--location DIR]  [--dbname DBNAME]  [DIR/DBNAME]

       br_bioflat.rb [--show-namespaces]  [--format=CLASS]

       br_bioflat.rb [--show-namespaces]  [--files file]

DESCRIPTION

       This manual page documents briefly the br_bioflat.rb.

       br_bioflat.rb is an OBDA flat file indexer.

OPTIONS

       --search  Search a database for keywords.

       --namespace	   --name
		 Only  valid  with the --search option. Set the search namespace.  You can set this option multiple times to specify more than one
		 namespace.

       --create  Create an index.

       --location
		 Specify the directory.

       --dbname  Specify the name of the database.

       --primary	   --secondary
		 Set the primary and secondarynamespace of the index. Default primary/secondary namespaces depend on the format of the	flatfiles.
		 Only valid with the --create option.

       --add-secondary
		 Add secondary namespaces to the default specification. You can use this option many times. Only valid with the --create option.

       --update  Update an index

       --sort	 Sort  an index. You can set this to a path to an external sorting program, or BUILTIN to use the builtin sort module. This option
		 is only valid with --create (or --update) and --type flat options.

       --renew	 Re-read all flatfiles and update whole index. This option is only valid with the --update option.

       --show-namespaces
		 Display the namespaces for an index file.

AUTHOR

       This manual page was written by David Nusinow dnusinow@debian.org for the Debian system (but may be used by others).  Permission is granted
       to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by
       the Free Software Foundation.

       On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

																	BIORUBY(1)