view release on metacpan or  search on metacpan

lib/Bio/Grep.pm  view on Meta::CPAN

   my $filter = MyFilter->new();

   $sbe->settings->filters( ( $filter ) );
   $sbe->search();

See L<Bio::Grep::Filter::FilterI>.

=head1 ERROR HANDLING

C<Bio::Grep> throws L<Bio::Perl> exceptions when errors occur. You can use the 
module L<Error> to catch these exceptions:

   use Error qw(:try);
  
   ...
  
   try {
       $sbe->search();
   } catch Bio::Root::SystemException with {
       my $E = shift;
       print STDERR 'Back-end call failed: ' .     
       $E->{'-text'} . ' (' .  $E->{'-line'} . ")\n";
       exit(1);    
   } catch Bio::Root::BadParameter with {
       my $E = shift;
       print STDERR 'Wrong Settings: ' .     
       $E->{'-text'} . ' (' .  $E->{'-line'} . ")\n";
       exit(1);    
   } otherwise {        
       my $E = shift;
       print STDERR "An unexpected exception occurred: \n$E";
       exit(1);  
   };

C<Bio::Grep> throws a C<SystemException> when a system() call failed,
C<BadParameter> whenever C<Bio::Grep> recognizes some problems in the settings.
Be aware that C<Bio::Grep> does not find all of these problems. In such a case,
the back-end call will fail and this module will throw a C<SystemException>.

Whenever it is not possible to open, copy, close, delete or
write a file, croak() (L<Carp>) is called.

See L<Bio::Root::Exception>, L<Carp>.

=head1 SECURITY

The use of this module (in Web Services for example) should be quite secure. All
test run in taint mode. C<Bio::Grep> checks the settings before it generates the string
for the system() call and uses L<File::Temp> for all temporary files.

However, keep in mind that it is quite B<easy to start a query that will run
forever> without any further settings check, especially with the C<RE>
back-end. So you should limit C<mismatches>, C<query_length> and all
other settings that have an significant impact on the calculation time.
You should also set C<maxhits>. 

=head1 INCOMPATIBILITIES

None reported.

=head1 BUGS AND LIMITATIONS

No bugs have been reported. 

There is not yet a nice interface for searching for multiple queries. However,
C<Vmatch> and C<GUUGle> support this feature. So you can generate a Fasta query file
with L<Bio::SeqIO> and then set C<$sbe-E<gt>settings-E<gt>query_file()>. To
find out, to which query a match belongs, you have to check C<$res-E<gt>query>.

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>

=head1 AUTHOR

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


=head1 LICENSE AND COPYRIGHT

Copyright (C) 2007-2009 by M. Riester.

Based on Weigel::Search v0.13, Copyright (C) 2005-2006 by Max Planck 
Institute for Developmental Biology, Tuebingen.

This module is free software; you can redistribute it and/or
modify it under the same terms as Perl itself.


=head1 DISCLAIMER OF WARRANTY

BECAUSE THIS SOFTWARE IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
FOR THE SOFTWARE, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
PROVIDE THE SOFTWARE "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER
EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE
ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS WITH
YOU. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL
NECESSARY SERVICING, REPAIR, OR CORRECTION.

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
REDISTRIBUTE THE SOFTWARE AS PERMITTED BY THE ABOVE LICENSE, BE