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Bio::Matrix::PSM::PsmHUserrContributed Perl DocBio::Matrix::PSM::PsmHeaderI(3)

NAME
       Bio::Matrix::PSM::PsmHeaderI - handles the header data from a PSM file

SYNOPSIS
	use Bio::Matrix::PSM::IO;
	#Obtain	an Bio::Matrix::PSM::IO	object:
	my $psmIO= Bio::Matrix::PSM::IO->new(-file=>$file, -format=>'mast');

	#Get some general data about the file you are parsing:
	my $release=$psmIO->release;
	my $version=$psmIO->version;

	print "This analysis was performed using MAST version $version,	release	$release\n";

	#Now let's see what are	the consensus sequences	of the motifs fed as an	input:
	my %seq=$psmIO->seq;

	#let's cycle through all consensus sequences now:

	foreach	my $id ($psmIO->hid) {
	  print	"Motif $id is \t",$seq{$id},"\n";
	}

	 #Finally look at the stuff we do not parse:
	 my @inputfile=grep(/datafile/i,$psmIO->unstructured);

DESCRIPTION
       Generally you should not	use this object	directly, you can access the
       information through a PSM driver	(See Bio::Matrix::PSM::IO). It is
       handling	the header data	from a PSM file	which may be very different.
       This means that some of the methods will	return undef naturally,
       because this information	is not present in the file which is parsed.
       Some important data might be left over in the unstructured part,	and
       you might have to parse it yourself. I will try to 'structure' this
       header more in the near future.

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 - Stefan	Kirov
       Email skirov@utk.edu

APPENDIX
   new
	Title	: new
	Usage	: my $header= Bio::Matrix::PSM::PsmHeader->new
		   ( -seq=>\%seq, -mid=>\%mid, -width=>\%width,
		     -instances=>\%instances, -header=>\@header, -type=>'mast');
	Function: Creates a new	Bio::Matrix::PSM::PsmHeader object
	Throws	:
	Example	:
	Returns	:  Bio::Matrix::PSM::PsmHeaderI	object
	Args	:  hash

   seq
	Title	: seq
	Usage	: my %seq= $header->seq();
	Function: Returns the sequence data as a hash, indexed by a
		  sequence ID (motif id	or accession number)
		  In case the input data is a motif it would return the
		  consenus seq for each	of them	(mast).
	Throws	:
	Example	:
	Returns	:  hash
	Args	:

   hid
	Title	: hid
	Usage	: my @ids= $header->hid();
	Function: Returns array	with the motif/instance	ids
	Throws	:
	Example	:
	Returns	:  array
	Args	:

   length
	Title	: length
	Usage	: my %length= $header->length();
	Function: Returns the length of	the input sequence or motifs as	a hash,	indexed
		  by a sequence	ID (motif id or	accession number)
	Throws	:
	Example	:
	Returns	:  hash
	Args	:

   instances
	Title	: instances
	Usage	: my %instances= $header->length();
	Function: Returns the instance,	used  as a hash, indexed
		  by a sequence	ID (motif id or	accession number)
	Throws	:
	Example	:
	Returns	:  hash	of Bio::Matrix::PSM::InstanceSite objects
	Args	:

   weights
	Title	: weights
	Usage	: my %weights= $header->weights();
	Function: Returns the weights of the input sequence as a hash, indexed
		  by a sequence	ID
	Throws	:
	Example	:
	Returns	:  hash
	Args	:

   unstuctured
	Title	: unstuctured
	Usage	: my @unstructured= $header->unstuctured();
	Function: Returns the unstructured data	in the header as an array, one line per
		  array	element, all control symbols are removed with \W
	Throws	:
	Example	:
	Returns	:   array
	Args	:

   version
	Title	: version
	Usage	: my $version= $header->version;
	Function: Returns the version of the file being	parsed if such exists
	Throws	:
	Example	:
	Returns	:  string
	Args	:

   revision
	Title	: revision
	Usage	: my $revision=	$header->revision;
	Function: Returns the revision of the file being parsed	if such	exists
	Throws	:
	Example	:
	Returns	:  string
	Args	:

   _check
	Title	: _check
	Usage	: if ($self->_check('weights') { #do something}	else {return 0;}
	Function: Checks if the	method called is aplicable to the file format
	Throws	:
	Example	:
	Returns	:  boolean
	Args	:  string

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

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Stefan Kirov | APPENDIX

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