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examples/bgrep  view on Meta::CPAN

set to a true value, then C<bgrep> will output A LOT OF debug text.

=head1 DEPENDENCIES

L<Bio::Grep>, L<Getopt::Long>, L<Pod::Usage>, L<File::Basename>

=head1 INCOMPATIBILITIES

None reported.

=head1 BUGS AND LIMITATIONS

No bugs have been reported. 

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

perldoc L<Bio::Grep>

lib/Bio/Grep.pm  view on Meta::CPAN

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()>.