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Chimaera-Matcher-1.01
River stage zero No dependents
++
/ Chimaera::Matcher

NAME

Chimaera::Matcher - An object to look for Chimaeric (Bovine) MHC sequences

VERSION

Version 1.01

SYNOPSIS

An object to check for possible chimaeric sequences in MHC sequencing studies.

Example usage....

    use Chimaera::Matcher;

    my $foo = Chimaera::Matcher->new( 'haplotype1' => $haplotype1, 'haplotype2' => $haplotype2);
    
    if ($foo->possible_chimaera($test_seq)) {
        printf("Could be a chimaera\n");
    }
    else {
        printf("Not a chimaera\n");
    }
    ...

SUBROUTINES/METHODS

new

Given a pair of sequence strings, construct a Matcher that we can use to test a series of possible chimaeric sequences against.

Two named sequence arguments must be supplied, keyed as 'haplotype1' and 'haplotype2'. Both must be the same length as each other and non-empty.

Tests are all case-insensitive.

possible_chimaera

Pass in a sequence to be tested as a possible chimaera. The sequence must be the same length as the haplotype arguments supplied in the constructor. If the test sequence has a base that was not seen in either of the haplotypes supplied, then it cannot be a chimaera of the two. If the test sequence switches from one haplotype to the other more than once, then this cannot be a chimaera.

If the test sequence is identical to one or other of the input haplotypes then it also cannot be defined as a chimaera.

AUTHOR

"Andy Law", <"andy.law at roslin.ed.ac.uk">

BUGS

Please report any bugs or feature requests to bug-chimaera at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Chimaera. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

SUPPORT

You can find documentation for this module with the perldoc command.

    perldoc Chimaera::Matcher

You can also look for information at:

ACKNOWLEDGEMENTS

LICENSE AND COPYRIGHT

Copyright 2015 The Roslin Institute.

This program is free software; you can redistribute it and/or modify it under the terms of the the Artistic License (2.0). You may obtain a copy of the full license at:

http://www.perlfoundation.org/artistic_license_2_0

Any use, modification, and distribution of the Standard or Modified Versions is governed by this Artistic License. By using, modifying or distributing the Package, you accept this license. Do not use, modify, or distribute the Package, if you do not accept this license.

If your Modified Version has been derived from a Modified Version made by someone other than you, you are nevertheless required to ensure that your Modified Version complies with the requirements of this license.

This license does not grant you the right to use any trademark, service mark, tradename, or logo of the Copyright Holder.

This license includes the non-exclusive, worldwide, free-of-charge patent license to make, have made, use, offer to sell, sell, import and otherwise transfer the Package with respect to any patent claims licensable by the Copyright Holder that are necessarily infringed by the Package. If you institute patent litigation (including a cross-claim or counterclaim) against any party alleging that the Package constitutes direct or contributory patent infringement, then this Artistic License to you shall terminate on the date that such litigation is filed.

Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.