bio::matrix::psm::instancesitei(3pm) [debian man page]
Bio::Matrix::PSM::InstanceSiteI(3pm) User Contributed Perl Documentation Bio::Matrix::PSM::InstanceSiteI(3pm)NAME
Bio::Matrix::PSM::InstanceSiteI - InstanceSite interface, holds an instance of a PSM
SYNOPSIS
use Bio::Matrix::PSM::InstanceSite;
#Y ou can get an InstanceSite object either from a file:
my ($instances,$matrix)=$SomePSMFile->parse_next;
#or from memory
my %params=(seq => 'TATAAT',
id => "TATAbox1",
accession => 'ENSG00000122304',
mid => 'TB1',
desc => 'TATA box, experimentally verified in PRM1 gene',
relpos => -35);
DESCRIPTION
Abstract interface to PSM site occurrence (PSM sequence match). InstanceSite objects may be used to describe a PSM (See
Bio::Matrix::PSM::SiteMatrix) sequence matches. The usual characteristic of such a match is sequence coordinates, score, sequence and
sequence (gene) identifier- accession number or other id. This object inherits from Bio::LocatableSeq (which defines the real sequence) and
might hold a SiteMatrix object, used to detect the CRE (cis-regulatory element), or created from this CRE. While the documentation states
that the motif id and gene id (accession) combination should be unique, this is not entirely true- there might be more than one occurrence
of the same cis-regulatory element in the upstream region of the same gene. Therefore relpos would be the third element to create a really
unique combination.
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Stefan Kirov
Email skirov@utk.edu
SEE ALSO
Bio::Matrix::PSM::SiteMatrix, Bio::Matrix::PSM::Psm, Bio::Matrix::PSM::IO
APPENDIX
mid
Title : mid
Usage : my $mid=$instance->mid;
Function: Get/Set the motif id
Throws :
Returns : scalar
Args : scalar
score
Title : score
Usage : my $score=$instance->score;
Function: Get/Set the score (mismatches) between the instance and the attached (or
initial) PSM
Throws :
Returns : real number
Args : real number
start
Title : start
Usage : my $start=$instance->start;
Function: Get/Set the position of the instance on the sequence used
Throws :
Returns : integer
Args : integer
relpos
Title : relpos
Usage : my $seqpos=$instance->relpos;
Function: Get/Set the relative position of the instance with respect to the transcription start
site (if known). Can and usually is negative.
Throws :
Returns : integer
Args : integer
minstance
Title : minstance
Usage : my $minstance=$misntance->score;
Function: Get/Set the unique identifier- sequence id/motif id, for example PRM1_TATAbox.
Not necessarily human readable.
Throws :
Returns : string
Args : string
perl v5.14.2 2012-03-02 Bio::Matrix::PSM::InstanceSiteI(3pm)
Check Out this Related Man Page
Bio::Matrix::PSM::PsmI(3pm) User Contributed Perl Documentation Bio::Matrix::PSM::PsmI(3pm)NAME
Bio::Matrix::PSM::PsmI - abstract interface to handler of site matricies
SYNOPSIS
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 bellow.
DESCRIPTION
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.
DESIGN ISSUES
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 beacause 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.
SEE ALSO
Bio::Matrix::PSM::SiteMatrix, Bio::Matrix::PSM::IO::meme, Bio::Matrix::PSM::IO::transfac, Bio::Matrix::PSM::InstanceSite
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Stefan Kirov
Email skirov@utk.edu
DISCLAIMER
This software is provided "as is" without warranty of any kind.
APPENDIX
new
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=>$sites)
Function: Creates a new Bio::Matrix::PSM::Psm object
Throws :
Example :
Returns : Bio::Matrix::PSM::Psm object
Args : hash
instances
Title : instances
Usage : my @instances=@{$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)
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
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 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...)
perl v5.14.2 2012-03-02 Bio::Matrix::PSM::PsmI(3pm)