Bio-Grep

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Changes  view on Meta::CPAN

          with up-/downstream regions

0.8.2  Tue Jul  31 16:11:00 2007
    - POD improvements 
    - more tests
    - code cleanup (Bio::Grep::Root)
    
0.8.1  Tue Jul  31 16:11:00 2007
    - POD improvements 
    - code cleanup
    - Cookbook
    - removed directory Container (unnecessary and confusing)
    - Error messages more consistent
    - more tests
    
0.8.0  Mon Jul  30 19:20:00 2007
    - POD improvements
    - direct_and_rev_com
    - RE back-end
    - use Fatal qw(open close), removed own exception handling
    - replaced global dirhandle in BackendI with local dirhandle

MANIFEST  view on Meta::CPAN

Changes
lib/Bio/Grep.pm
lib/Bio/Grep/Benchmarks.pod
lib/Bio/Grep/Cookbook.pod
lib/Bio/Grep/Root.pm
lib/Bio/Grep/Backend/Agrep.pm
lib/Bio/Grep/Backend/BackendI.pm
lib/Bio/Grep/Backend/GUUGle.pm
lib/Bio/Grep/Backend/Vmatch.pm
lib/Bio/Grep/Backend/RE.pm
lib/Bio/Grep/SearchResult.pm
lib/Bio/Grep/SearchSettings.pm
lib/Bio/Grep/Filter/FilterI.pm
lib/Bio/Grep/Filter/FilterRemoveDuplicates.pm

README  view on Meta::CPAN

DOCUMENTATION


1. Tutorials
------------

bgrep is an example implementation. The source code is well documented, so
maybe it is a good starting point.

A not yet comprehensive cookbook is available in perldoc Bio::Grep::Cookbook.
Please contribute recipes if you can!


2. Performance
--------------

2.1 Vmatch


*  Try $sbe->settings->showdesc(200) if you don't need upstream or downstream

TODO  view on Meta::CPAN

 - filter priority (fast filters like FilterRemoveDuplicates should run first 
   automatically)
 - interface for multiple queries [ ?? ]
 - support other file formats (Genbank,...) and input sources (maybe even
   databases?) [ DONE ]
 - support agreps regular expressions 
 - support agrep query_file
 - create a simple backend that does not require additional software [ DONE ]
 - remove EMBOSS and bioperl-run, add own alignment calculation 
 - cleanup testcases [ STARTED ]
 - Bio::Grep::Cookbook [ STARTED ]

Post 1.0

 - configfile for bgrep
 - New Back-ends: 
     * PoSSuM back-end [ ?? ]
     * Seqan library [ ?? ]
 - contribute parsers to Bio::Tools::Run    

lib/Bio/Grep.pm  view on Meta::CPAN

checks the settings carefully before calling back-ends. See L<"SECURITY">.

=back

=head1 QUICK START

This is only a short overview of the functionality of this module.
You should also read L<Bio::Grep::Backend::BackendI> and the documentation of
the back-end you want to use (e.g. L<Bio::Grep::Backend::Vmatch>).

L<Bio::Grep::Cookbook> is a (not yet comprehensive) collection of recipes for
common problems.

=head2 GENERATE DATABASES 

As a first step, you have to generate a C<Bio::Grep> database out of your Fasta
file in which you want to search. A C<Bio::Grep> database consists of a couple of
files and allows you to retrieve information about the database as well
as to perform queries as fast and memory efficient as possible. You have to do
this only once for every file.

lib/Bio/Grep.pm  view on Meta::CPAN

It is likely that C<$sbe-E<gt>settings-E<gt>query> is renamed to C<queries()>.

Please report any bugs or feature requests to
C<bug-bio-grep@rt.cpan.org>, or through the web interface at
L<http://rt.cpan.org>. 


=head1 SEE ALSO

L<Bio::Grep::Cookbook>
L<Bio::Grep::Backend::BackendI>
L<Bio::Grep::Backend::Vmatch>
L<Bio::Grep::Backend::GUUGle>
L<Bio::Grep::Backend::RE>
L<Bio::Grep::Backend::Agrep>
L<Bio::Grep::Benchmarks>

=head2 PUBLICATIONS

C<GUUGle>: L<http://bioinformatics.oxfordjournals.org/cgi/content/full/22/6/762>

lib/Bio/Grep/Cookbook.pod  view on Meta::CPAN

=head1 NAME

Bio::Grep::Cookbook - Bio::Grep Cookbook

=head1 DESCRIPTION

This collection of recipes intends to provide you solutions for the most
common problems and to make the development process easier. 

=head1 RECIPES


All recipes assume that the database is generated in the directory I<data>.

lib/Bio/Grep/Cookbook.pod  view on Meta::CPAN

Note that the search for exact matches is fast with Vmatch, so the enumeration
of all possible motifs (Solution A) can often be the best method.

=back

=head1 FEEDBACK

Have you solved your (not too exotic ;)) problem with L<Bio::Grep> and a
solution is not yet listed here? Contribute it to this
Cookbook!

Please report any bugs, feature requests and recipes to
C<bug-bio-grep@rt.cpan.org>, or through the web interface at
L<http://rt.cpan.org>. 


=head1 AUTHOR

Markus Riester, E<lt>mriester@gmx.deE<gt>

t/50.synopsis.t  view on Meta::CPAN

 
  $sbe->search({
     datapath   => 't/data',
     database   => 'ATH1.cdna',
     query_file => 'motifs.fasta',
     complete   => 1,
  });

EOT
;
    ok(!code_eval($code),"Cookbook recipe motifs solution a compiles") || diag $@;

    unlink 'motifs.fasta';
}

# Agrep
$backendname  = 'Agrep';

SKIP:{

    skip 'Agrep binary not in path', 1 if

t/50.synopsis.t  view on Meta::CPAN

  my $motif = '[AC]{4}TAAAA[AGCT]GG';
 
  $sbe->search({
     datapath  => 't/data',
     database  => 'Test_DB_RevCom.fasta',
     query      => $motif,
  });
EOT
;
eval $code;
ok(!$@,"Cookbook recipe motifs solution b compiles") || diag $@;

$code = 'bllll';
eval $code;
ok(code_eval($code),"bllll not compiles");

delete_files;
rmdir('t/tmp');
rmdir('t/data');
rmdir('t/data2');