Bio::Grep::Root - Superclass for all Bio::Grep* packages
This superclass adds some useful methods to all Bio::Grep packages.
See Bio::Root::Root for inherited methods.
is_integer($var_to_check, 'Description')
Returns the variable, but it is now not tainted anymore. Throws an exception if the specified variable is not an integer. If a second argument is passed, it will be used in the exception text.
is_word($var_to_check, 'Description')
Returns the variable, but it is now not tainted anymore. Throws an exception if the specified variable is not a word. If a second argument is passed, it will be used in the exception text.
is_path($var_to_check, 'Description')
Returns the variable, but it is now not tainted anymore. Throws an exception if the specified variable is not a valid path (It is word but accepts also '/'). If a second argument is passed, it will be used in the exception text.
is_sentence($var_to_check, 'Description')
Returns the variable, but it is now not tainted anymore. Throws an exception if the specified variable is not a valid sentence (It is word but accepts also '/:,;|'). If a second argument is passed, it will be used in the exception text.
WARNING: make sure that command line arguments are quoted ( my $command = "... '$sentence' ")
is_arrayref_of_size($a_ref, $size)
Checks if $a_ref is an array reference and the array is of size $size or larger.
... looks not valid.
Some variable does not match the specified regular expression. Bio::Root::BadParameter.
Bio::Root::BadParameter
Argument is not an array reference.
Method is_arrayref_of_size() is used to check arguments. You probably called a method with wrong arguments.
Missing arguments: require hash with keys "regex" ...
You called the internal method _check_variable() without a valid hashref. Don't use this method. Bio::Root::BadParameter.
Size of argument is too small.
Method is_arrayref_of_size() is used to check arguments. You probably called a method with missing arguments.
Unknown regex.
You called the internal method _check_variable() with an invalid regex. Don't use this method. Bio::Root::BadParameter.
Markus Riester, <mriester@gmx.de>
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.
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.
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To install Bio::Grep, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Grep
CPAN shell
perl -MCPAN -e shell install Bio::Grep
For more information on module installation, please visit the detailed CPAN module installation guide.