Provided by: libbio-perl-perl_1.7.2-2_all 
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