Lincoln D. Stein > GBrowse > docs/pod/README-lucegene.pod

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Using the Lucene Bio::DB::GFF Adaptor ^

The Bio::DB::GFF "lucene" adaptor to support Lucene-indexed GFF files is a contribution to GBrowse version 1.63 from the GMOD LuceGene project.

SYNOPSIS ^

   # Generate a lucene index this way
   bp_load_gff.pl --adaptor lucene --create \
      --dsn $HTDOCS/gbrowse/databases/yeast_lucene \
      $HTDOCS/gbrowse/sample_data/yeast_data.gff

   # The basic GBrowse gbrowse.conf/ adaptor entry is
   db_adaptor    = Bio::DB::GFF
   db_args       = -adaptor lucene
       -dsn '$HTDOCS/gbrowse/databases/yeast_lucene'

  where $HTDOCS is full path to {Generic-Genome-Browser}/htdocs

DESCRIPTION ^

This adaptor allows you to run GBrowse with fast indexed GFF files without the administrative overhead of MySQL or PostgreSQL. Lucene is a Java Apache open-source project with very high performance for searching large text databases. It runs as fast or somewhat faster than the BerkeleyDB and MySQL adaptors. It is easy to install and use.

The indices generated are platform-independent, unlike BerkeleyDB. Thus GFF data, indices, the Lucene software can be copied and used without special installation, compiling, data-reindexing among any computers with Java.

INSTALLATION ^

You should have installed and tested GBrowse, version 1.63 or later. Fetch this adaptor software from ftp://ftp.eugenes.org/eugenes/gbrowse/lucene-gbrowse-lite.zip (This will also be available thru http://www.gmod.org/lucegene/)

Unzip and place these in {Generic-Genome-Browser}/lib/java/ lib/java/lucene.jar , LuceneIndexer.class, LuceneSearcher.class

Place these either in {Generic-Genome-Browser}/lib/Bio/DB/GFF/Adaptor/ or where you have installed other BioPerl Bio/DB/GFF/Adaptor/ . lib/Bio/DB/GFF/Adaptor/lucene.pm , LuceneFasta.pm

Make sure this lib is in your PERL path for bp_load_gff.pl and Gbrowse. See the PerlDoc in lucene.pm for further information.

There is a simple socket server, LuceneSocket, to replace command-line invocation of Lucene. Benchmarks show that it does not improve speed over the command-line invocation, so it is not recommended. See the PerlDoc in lucene.pm for more information.

LOADING DATA ^

The BioPerl script bp_load_gff.pl will work with this lucene adaptor like it does with berkeleydb, mysql and other Bio::DB::GFF adaptors. The only option needed once Perl and Java parts are installed as above, is to use '--adaptor lucene' in place of other adaptor options. The '--dsn /path/to/index' option will create a Lucene index at the identified path (with --create), or update an existing index when using --write flag.

If your input includes FastA sequence, it will will be indexed into the same Lucene index as the GFF data. A FastA sequence file will be created in the same --dsn folder, like with the BerkeleyDB adaptor.

Once an index is created, it can be updated and added to (either with new GFF or FastA), using the --write option.

A current limitation is the lack of "delete" options. If you need to remove features, you now must recreate the index.

USING WITH GBROWSE ^

The only gbrowse.conf change for this adaptor is the '-adaptor lucene' addition to db_args. Otherwise it works like the BerkeleyDB adaptor (see section 19 of the tutorial for BerkeleyDB; docs/tutorial/tutorial.html).

The "lib/java/" Java parts must be findable by lucene.pm. If these are in the Perl @INC path, or in a 'java/' subfolder of @INC, they will be found. Alternately set environ variable JAVA_LIB. The Perl module calls the Java LuceneSearcher or LuceneIndexer application thru a perl IO pipe, a standard operation.

Internally, the lucene.pm adaptor is a subclass of the berkeleydb.pm and memory.pm adaptors. It interfaces with GBrowse the same way, and should return th same features as these and MySQL, etc. for the same input data (tests show it does; let the author know if you find otherwise).

It handles searches, especially of GFF attributes and notes, somewhat differently, relying on Lucene text search syntax and abilities. It generally will find matches to any word-like terms that exist in the input data, and supports '*' and '?' trailing wild-cards, but not leading wild cards ('*something' is not allowed). Lucene provides very capable phrase searches, so complex terms are matched. The current configuration uses case-insensitive index and search. The module may need some tuning as it matures to produce the most appropriate results from notes and attributes searches.

SEE ALSO ^

The server ftp://ftp.eugenes.org/eugenes/gbrowse/ has a set of Lucene indices of genomes for Worm, Yeast, Rice, and 9 Fruitfly species, along with Gbrowse configuration files. You should be able to copy these, add to Gbrowse the Lucene-lite and Lucegene adaptors, and display the genomes from your favorite server computer.

Information on Lucene is at http://www.gmod.org/lucegene/, http://lucene.apache.org/

AUTHORS ^

Don Gilbert <gilbertd@indiana.edu> August 2005

Adapted from Bio::DB::GFF::Adaptor::berkeleydb of Vsevolod (Simon) Ilyushchenko >simonf@cshl.edu< and Lincoln Stein >lstein@cshl.edu<

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