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Bio::Matrix::PSM::ProtUser3Contributed Perl DocumeBio::Matrix::PSM::ProtPsm(3)

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
       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.

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

perl v5.24.1			  2017-07-08	  Bio::Matrix::PSM::ProtPsm(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - James Thompson | DISCLAIMER | SEE ALSO | APPENDIX

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