Bio::Matrix::PSM::PsmI - abstract interface to handler of site matricies
use Bio::Matrix::PSM::IO;
# To get a Psm object from a file use the Psm parser:
my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'meme', -file=>$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
}
}
# or create from memmory:
my $psm= Bio::Matrix::PSM::Psm->new( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,-pT=>\@pT,
-id=>$id,
-instances=>$instances, -e_val=>$e_val,
-IC=>$ic, -width=>$width, -sites=>$sites)
# where pA through pG are the respective frequencies of the matrix (see also
# Bio::Matrix::PSM::SiteMatrix), and everything else is self-explenatory,
# except for
#-instances (reference to an array of Bio::Matrix::PSM::InstanceSite objects)
# which is documented below.
Supposed to handle a combination of site matrices and/or their corresponding
sequence matches (instances). This object inherits from
Bio::Matrix::PSM::SiteMatrix, so you can use the respective methods. It may
hold also an array of Bio::Matrix::PSM::InstanceSite object, but you will have
to retrieve these through Bio::Matrix::PSM::Psm->instances method (see
below). To some extent this is an expanded SiteMatrix object, holding data
from analysis that also deal with sequence matches of a particular matrix.
This design is a bit of a compromise, so it might be a temporary solution 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.
Bio::Matrix::PSM::SiteMatrix, Bio::Matrix::PSM::IO::meme,
Bio::Matrix::PSM::IO::transfac, Bio::Matrix::PSM::InstanceSite
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Title : new
Usage : my $psm= Bio::Matrix::PSM::Psm->new( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,
-pT=>\@pT,-id=>$id,
-instances=>$instances,
-e_val=>$e_val,
-IC=>$ic, -width=>$width,
-sites=>$sites)
Function: Creates a new Bio::Matrix::PSM::Psm object
Throws :
Example :
Returns : Bio::Matrix::PSM::Psm object
Args : hash
Title : instances
Usage : my @instances=@{$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)
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
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 undef 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...)