Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::Matrix::PSM::ProtPsm - handle combination of site matricies

SYNOPSIS

         use Bio::Matrix::PSM::IO;

         #To get a ProtPsm object from a file use the Psm parser:
         my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'psiblast', -file=>$file);

         # Now go through all entities in the file with next_psm, which
         # returns a Psm object see Bio::Matrix::PSM::IO for detailed
         # documentation (matrix predictions or matrix sequence matches or
         # both):

         while (my $psm=$psmIO->next_psm) {
            my %psm_header = $psm->header;
            my $ic    = $psm_header{IC};
            my $sites = $psm_header{sites};
            my $width = $psm_header{width};
            my $score = $psm_header{e_val};
            my $IUPAC = $psm->IUPAC;
            my $instances = $psm->instances;
            foreach my $instance (@{$instances}) {
              my $id = $instance->primary_id;
              #Do something with the id
            }
          }

DESCRIPTION

       To handle a combination of site matrices and/or their corresponding sequence matches
       (instances). This object inherits from Bio::Matrix::PSM::ProtMatrix, so you can methods
       from that class. It may hold also an array of Bio::Matrix::PSM::InstanceSite object, but
       you will have to retrieve these through Bio::Matrix::PSM::ProtPsm->instances method (see
       below). To some extent this is an expanded ProtMatrix object, holding data from analysis
       that also deal with sequence matches of a particular matrix.

   DESIGN ISSUES
       This does not make too much sense to me I am mixing PSM with PSM sequence matches Though
       they are very closely related, I am not satisfied by the way this is implemented here.
       Heikki suggested different objects when one has something like meme But does this mean we
       have to write a different objects for mast, meme, transfac, theiresias, etc.?  To me the
       best way is to return SiteMatrix object + arrray of InstanceSite objects and then mast
       will return undef for SiteMatrix and transfac will return undef for InstanceSite. Probably
       I cannot see some other design issues that might arise from such approach, but it seems
       more straightforward.  Hilmar does not like this because it is an exception from the
       general BioPerl rules. Should I leave this as an option?  Also the header rightfully
       belongs the driver object, and could be retrieved as hashes.  I do not think it can be
       done any other way, unless we want to create even one more object with very unclear
       content.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably
        to one of the Bioperl mailing lists.  Your participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - James Thompson

       Email tex@biosysadmin.com

DISCLAIMER

       This software is provided "as is" without warranty of any kind.

SEE ALSO

       ProtMatrix, meme, transfac, psiblast, InstanceSite

APPENDIX

   new
        Title   : new
        Usage   : my $psm = Bio::Matrix::PSM::ProtPsm->new(
                     -pS => [ '0', '33', '0', '16', '1', '12', '11', '25' ],
                     -pF => [ '0', '0', '2', '0', '3', '0', '0', '0' ],
                     -pT => [ '0', '8', '7', '10', '1', '2', '7', '8' ],
                     -pN => [ '0', '0', '2', '13', '0', '36', '1', '4' ],
                     -pK => [ '0', '5', '0', '13', '1', '15', '0', '2' ],
                     -pY => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
                     -pE => [ '0', '41', '1', '12', '0', '0', '0', '15' ],
                     -pV => [ '0', '3', '9', '0', '2', '0', '3', '1' ],
                     -pQ => [ '0', '0', '0', '15', '0', '4', '0', '3' ],
                     -pM => [ '100', '0', '66', '0', '2', '0', '0', '0' ],
                     -pC => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
                     -pL => [ '0', '0', '8', '0', '25', '0', '4', '0' ],
                     -pA => [ '0', '10', '1', '9', '2', '0', '22', '16' ],
                     -pW => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
                     -pP => [ '0', '0', '0', '0', '3', '1', '45', '0' ],
                     -pH => [ '0', '0', '0', '0', '0', '0', '1', '0' ],
                     -pD => [ '0', '0', '1', '7', '2', '2', '0', '22' ],
                     -pR => [ '0', '0', '0', '3', '0', '27', '0', '0' ],
                     -pI => [ '0', '0', '3', '0', '59', '1', '2', '3' ],
                     -pG => [ '0', '0', '0', '1', '0', '0', '4', '1' ],
                     -IC => $ic,
                     -sites => $istes,
                     -width => $width,
                     -e_val => $e_val,
                     -instances => $instances,
                  }

        Function: Creates a new Bio::Matrix::PSM::ProtPsm object
        Throws  :
        Example :
        Returns :  Bio::Matrix::PSM::Psm object
        Args    :  hash

   instances
        Title   : instances
        Usage   :   my @instances=@{$psm->instances};
        Function: Gets/sets the instances (Bio::Matrix::PSM::InstanceSite objects)
               associated with the Psm object
        Throws  :
        Example :
        Returns :  array reference (Bio::Matrix::PSM::InstanceSite objects)
        Args    :  array reference (Bio::Matrix::PSM::InstanceSite objects)

   header
        Title   : header
        Usage   :  my %header=$psm->header;
               my $ic=$psm->header('IC');
        Function: Gets the general information, common for most files,
              dealing with PSM such as information content (IC), score
              (e-value, etc.), number of sites (sites) and width. This
              list may expand. The current list should be in
              @Bio::Matrix::PSM::Psm::HEADER. Returns an epty list if an
              argument is supplied that is not in
              @Bio::Matrix::PSM::meme::HEADER.
        Throws  :
        Example :
        Returns :  hash or string
        Args    :  string (IC, e_val...)

   matrix
        Title   :  matrix
        Usage   :  my $matrix = $psm->matrix;
        Function:  Gets/sets the SiteMatrix related information
        Throws  :
        Example :
        Returns :  Bio::Matrix::PSM::SiteMatrix objects
        Args    :  Bio::Matrix::PSM::SiteMatrix objects