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)

Bio::Matrix::PSM::IO(3pm)				User Contributed Perl Documentation				 Bio::Matrix::PSM::IO(3pm)

NAME

       Bio::Matrix::PSM::IO - PSM parser

SYNOPSIS

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

	 my $psmIO= Bio::Matrix::PSM::IO->new(-file=>$file, -format=>'transfac');

	 my $release=$psmIO->release; #Using Bio::Matrix::PSM::PsmHeader methods

	 my $release=$psmIO->release;

	 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;
	 }

DESCRIPTION

       This module allows you to read DNA position scoring matrices and/or their respective sequence matches from a file.

       There are two header methods, one belonging to Bio::Matrix::PSM::IO::driver and the other to Bio::Matrix::PSM::Psm. They provide general
       information about the file (driver) and for the current PSM result (Psm) respectively. Psm header method always returns the same thing, but
       some values in the hash might be empty, depending on the file you are parsing. You will get undef in this case (no exceptions are thrown).

       Please note that the file header data (commenatries, version, input data, configuration, etc.)  might be obtained through
       Bio::Matrix::PSM::PsmHeader methods. Some methods are driver specific (meme, transfac, etc.): meme: weight mast: seq, instances

       If called when you parse a different file type you will get undef. For example:

	 my $psmIO= Bio::Matrix::PSM::IO->new(file=>$file, format=>'transfac');
	 my %seq=$psmIO->seq;

       will return an empty hash. To see all methods and how to use them go to Bio::Matrix::PSM::PsmHeaderI.

       See also Bio::Matrix::PSM::PsmI for details on using and manipulating the parsed data.

       The only way to write PFM/PWM is through masta module (something like fasta for DNA matrices). You can see an example by reading
       Bio::Matrix::PSM::IO::masta documentation.

See also
       Bio::Matrix::PSM::PsmI, Bio::Matrix::PSM::PsmHeaderI, Bio::Matrix::PSM::IO::masta

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

APPENDIX

   new
	Title	: new
	Usage	: my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'meme',
							-file=>$file);
	Function: Associates a file with the appropriate parser
	Throws	: Throws if the file passed is in HTML format or
		  if some criteria for the file
		  format are not met. See L<Bio::Matrix::PSM::IO::meme> and
		  L<Bio::Matrix::PSM::IO::transfac> for more details.
	Example :
	Returns : psm object, associated with a file with matrix file
	Args	: hash

   fh
	Title	: fh
	Usage	: $obj->fh
	Function: Get a filehandle type access to the matrix parser
	Example : $fh = $obj->fh;      # make a tied filehandle
		  $matrix = <$fh>;     # read a matrix object
	Returns : filehandle tied to Bio::Matrix::PSM::IO class
	Args	: none

   _load_format_module
	Title	: _load_format_module
	Usage	: *INTERNAL Matrix::PSM::IO stuff*
	Function: Loads up (like use) a module at run time on demand

   _guess_format
	Title	: _guess_format
	Usage	: $obj->_guess_format($filename)
	Returns : guessed format of filename (lower case)
	Args	: filename

   next_psm
	Title	: next_psm
	Usage	: my $psm=$psmIO->next_psm();
	Function: Reads the next PSM from the input file, associated with this object
	Throws	: Throws if there ara format violations in the input file (checking is not
		   very strict with all drivers).
	Example :
	Returns : Bio::Matrix::PSM::Psm object
	Args	: none

   _parseMatrix
	Title	: _parseMatrix
	Usage	:
	Function: Parses the next site matrix information in the meme file
	Throws	:
	Example :  Internal stuff
	Returns :  hash as for constructing a SiteMatrix object (see SiteMatrixI)
	Args	:  string

   _parseInstance
	Title	: _parseInstance
	Usage	:
	Function: Parses the next sites instances from the meme file
	Throws	:
	Example : Internal stuff
	Returns : Bio::Matrix::PSM::SiteMatrix object
	Args	: array references

   _parse_coordinates
	Title	: _parse_coordinates
	Usage	:
	Function:
	Throws	:
	Example : Internal stuff
	Returns :
	Args	:

   header
	Title	: header
	Usage	:  my %header=$psmIO->header;
	Function:  Returns the header for the PSM file, format specific
	Throws	:
	Example :
	Returns :  Hash or a single string with driver specific information
	Args	:  none

   _make_matrix
	Title	: _make_matrix
	Usage	:
	Function: makes a matrix from 4 array references (A C G T)
	Throws	:
	Example :
	Returns : SiteMatrix object
	Args	: array of references(A C G T)

perl v5.14.2							    2012-03-02						 Bio::Matrix::PSM::IO(3pm)