# Flat Databases HOWTO

Lincoln
Stein
Cold Spring Harbor Laboratory

    	  lstein-at-cshl.org

Brian
Osborne

Bioperl contributor

Cognia Corporation

              brian-at-cognia.com

Heikki
Lehväslaiho

Bioperl contributor

European Bioinformatics Institute

              heikki-at-ebi.co.uk

2003-02-26
1.0
2003-02-26
LS
First version
1.1
2003-10-17
BS
fom text into howto
1.2
2003-10-17
HL
fom txt reformatted into SGML

This document is copyright Lincoln Stein, 2002. For reproduction other than personal use please contact lstein at cshl.org

The Open Biological Database Access (OBDA) standard specifies a way of generating indexes for entry-based sequence files (e.g. FASTA, EMBL) so that the entries can be looked up and retrieved quickly. These indexes are created and accessed using the `Bio::DB::Flat` module.

## Creating OBDA-Compliant Indexed Sequence Files

`Bio::DB::Flat` has the same functionality as the various `Bio::Index` modules. The main reason to use it is if you want to use the BioSequence Registry system (see the OBDA Access HOWTO at http://bioperl.org/HOWTOs), or if you want to share the same indexed files among scripts written in other languages, such as those written with BioJava or BioPython.

There are four steps to creating a `Bio::DB::Flat` database:

1. Select a Root Directory

   Select a directory in which the flat file indexes will be stored. This directory should be writable by you, and readable by everyone who will be running applications that access the sequence data.

2. Move the Flat Files Into a Good Location

   The indexer records the path to the source files (e.g. FASTA, or local copies of GenBank, Embl or SwissProt). This means that you must not change the location or name of the source files after running the indexer. Pick a good stable location for the source files and move them there.

3. Choose a Symbolic Name for the Database

   Choose a good symbolic name for the database. For example, if you are mirroring GenBank, "genbank" might be a good choice. The indexer will create files in a subdirectory by this name located underneath the root directory.

4. Run the bioflat_index.pl script to load the sequence files into the database.

   The final step is to run the bioflat_index.PLS script. This script is located in the BioPerl distribution, under scripts/DB. For convenience, you are offered the option to copy it to /usr/bin or another system-wide directory on 'make install' (and its name will be changed to bioflat_index.pl).

## Choosing Your Options

The first time you run the script, the typical usage is as follows:

         bioflat_index.pl -c -l /usr/share/biodb -d genbank -i bdb -f fasta data/*.fa

The following command line options are required:

###

Option | Describtion
--- | ---
-c | create a new index
-l | path to the root directory
-d | symbolic name for the new database
-i | indexing scheme (discussed below)
-f | source file format

The `-c` option must be present to create the database. If the database already exists, `-c` will reinitialize the index, wiping out its current contents.

The `-l` option specifies the root directory for the database indexes.

The `-d` option chooses the symbolic name for the new database. If the `-c` option is specified, this will cause a new directory to be created underneath the root directory.

The `-i` option selects the indexing scheme. Currently there are two indexing schemes supported: "bdb" and "flat." "bdb" selects an index based on the Berkeley DB library. It is generally the faster of the two, but it requires that the Berkeley DB library (from Linux RPM or from www.sleepycat.com, version 2 or higher) and the Perl BerkeleyDB module be installed on your system. The Perl DB_File module will not work.

"flat" is a sorted text-based index that uses a binary search algorithm to rapidly search for entries. Although not as fast as bdb, the flat indexing system has good performance for even large databases, and it has no requirements beyond Perl itself. Once an indexing scheme has been selected there is no way to change it other than recreating the index from scratch using the `-c` option.

The `-f` option specifies the format of the source database files. It must be one of the many formats that BioPerl supports, including "genbank", "swiss", "embl" or "fasta". Consult the `Bio::SeqIO` documentation for the complete list. All files placed in the index must share the same format.

The indexing script will print out a progress message every 1000 entries, and will report the number of entries successfully indexed at the end of its run.

To update an existing index run bioflat_index.pl without the `-c` option and list the files to be added or reindexed. The `-l` and `-d` options are required, but the indexing scheme and source file format do not have to be specified for updating as they will be read from the existing index.

For your convenience, bioflat_index.pl will also take default values from the following environment variables:

###

ENV variable | description
--- | ---
OBDA_FORMAT | format of sequence file (`-f`)
OBDA_LOCATION | path to directory in which index files are stored (`-l`)
OBDA_DBNAME | name of database (-d)
OBDA_INDEX | type of index to create (`-i`)

## Moving Database Files

If you must change the location of the source sequence files after you create the index, there is a way to do so. Inside the root directory you will find a subdirectory named after the database, and inside that you will find a text file named "config.dat." An example config.dat is shown here:

         index	flat/1
         fileid_0	/share/data/alnfile.fasta	294
         fileid_1	/share/data/genomic-seq.fasta	171524
         fileid_2	/share/data/hs_owlmonkey.fasta	416
         fileid_3	/share/data/test.fasta	804
         fileid_4	/share/data/testaln.fasta	4620
         primary_namespace	ACC
         secondary_namespaces	ID
         format	URN:LSID:open-bio.org:fasta

For each source file you have moved, find its corresponding "fileid" line and change the path. Be careful not to change anything else in the file or to inadvertently replace tab characters with spaces.

# More information

For more information on using your indexed flat files please see the OBDA Access HOWTO.