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SmotifTF-0.09
River stage zero No dependents
++
/ RankSmotifs

NAME

RankSmotifs

VERSION

Version 0.01

SYNOPSIS

    Subroutines to rank smotifs based on e-values obtained from HMM comparisons. 

    use RankSmotifs;

    rank_all_smotifs($pdbcode);

EXPORT

    rank_all_smotifs
    find_ranks_by_evalue

SUBROUTINES

    rank_all_smotifs
    find_ranks_by_evalue

rank_all_smotifs

Script to rank smotifs in the database by their e-values

INPUT ARGUMENTS 1) $pdbcode : 4-letter pdbcode

INPUT FILES In the <pdbcode> folder: 1) dd_shiftcands<pdbcode><motnum>_<looplength><smotif type>.csv : Files containing results of comparing the query smotifs against the database.

OUTPUT FILES In the <pdbcode> folder: 1) <pdbcode>_motifs_best.csv : File containing a list of smotif candidates for each query smotif in the unknown protein 2) <pdbcode>_motifs_rmsd.csv : File containing rmsds of smotif candidates for each query smotif in the unknown protein.

    die "rank_smotifs: no file like dd_shiftcands$pdbcode* was found in $pdbcode"
        unless @found;
    # Let's assume that just ONE file like $pdbcode/$nam*csv was found.
    # $nam2  = 1aab/shiftcands1aab_01_8HH.csv
    my $nam2 = $found[0];

find_ranks_by_evalue

Subroutine to rank all the evaluated candidates for a single query smotif

AUTHORS

Fiserlab members, <andras at fiserlab.org>

BUGS

Please report any bugs or feature requests to bug-. at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=..

SUPPORT

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

    perldoc RankSmotifs

LICENSE AND COPYRIGHT

Copyright 2015 Brinda Vallat, Vilas Menon .

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.