.TH "BIORUBY" "1" 
.SH "NAME" 
br_bioflat.rb \(em OBDA flat file indexer 
.SH "SYNOPSIS" 
.PP 
Search: 
.PP 
\fBbr_bioflat.rb\fR [\fB\-\-search\fP]  [\fBoptions...\fP]  
.PP 
\fBbr_bioflat.rb\fR [\fB\-\-search\fP]  [\-\-location \fIDIR\fR]  [\-\-dbname \fIDBNAME\fR]  [\fBoptions...\fP]  [\fIKEYWORDS\fR]  
.PP 
Create index: 
.PP 
\fBbr_bioflat.rb\fR [\fB\-\-create\fP]  [\fB\-\-location \fIDIR\fR\fP]  [\fB\-\-dbname \fIDBNAME\fR\fP]  [\fB\-\-format \fIgenbank|embl|fasta\fR\fP]  [\fBoptions...\fP]  [\fB\-\-files \fIFILES...\fR\fP]  
.PP 
Update index: 
.PP 
\fBbr_bioflat.rb\fR [\fB\-\-update\fP]  [\fB\-\-location \fIDIR\fR\fP]  [\fB\-\-dbname \fIDBNAME\fR\fP]  [\fBoptions...\fP]  [\fB\-\-files \fIFILES...\fR\fP]  
.PP 
Show namespaces: 
.PP 
\fBbr_bioflat.rb\fR [\fB\-\-show-namespaces\fP]  [\fB\-\-location \fIDIR\fR\fP]  [\fB\-\-dbname \fIDBNAME\fR\fP]  [\fB\fIDIR/DBNAME\fR\fP]  
.PP 
\fBbr_bioflat.rb\fR [\fB\-\-show-namespaces\fP]  [\fB\-\-format=\fICLASS\fR\fP]  
.PP 
\fBbr_bioflat.rb\fR [\fB\-\-show-namespaces\fP]  [\fB\-\-files \fIfile\fR\fP]  
.SH "DESCRIPTION" 
.PP 
This manual page documents briefly the 
\fBbr_bioflat.rb\fR. 
.PP 
\fBbr_bioflat.rb\fR is an OBDA flat file indexer. 
.SH "OPTIONS" 
.IP "\fB\-\-search\fP         " 10 
Search a database for keywords. 
.IP "\fB\-\-namespace\fP 		\fB\-\-name\fP         " 10 
Only valid with the \-\-search option. Set the search namespace. 
You can set this option multiple times to specify more than one 
namespace. 
.IP "\fB\-\-create\fP         " 10 
Create an index. 
.IP "\fB\-\-location\fP         " 10 
Specify the directory. 
.IP "\fB\-\-dbname\fP         " 10 
Specify the name of the database. 
.IP "\fB\-\-primary\fP 		\fB\-\-secondary\fP         " 10 
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. 
.IP "\fB\-\-add-secondary\fP         " 10 
Add secondary namespaces to the default specification. You can 
use this option many times. Only valid with the \-\-create option. 
.IP "\fB\-\-update\fP         " 10 
Update an index 
.IP "\fB\-\-sort\fP         " 10 
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. 
.IP "\fB\-\-renew\fP         " 10 
Re-read all flatfiles and update whole index. This option is 
only valid with the \-\-update option. 
.IP "\fB\-\-show-namespaces\fP         " 10 
Display the namespaces for an index file. 
.SH "AUTHOR" 
.PP 
This manual page was written by David Nusinow dnusinow@debian.org for 
the \fBDebian\fP 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. 
 
.PP 
On Debian systems, the complete text of the GNU General Public 
License can be found in /usr/share/common-licenses/GPL. 
 
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