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bio::matrix::scoring(3pm) [debian man page]

Bio::Matrix::Scoring(3pm)				User Contributed Perl Documentation				 Bio::Matrix::Scoring(3pm)

NAME

       Bio::Matrix::Scoring - Object which can hold scoring matrix information

SYNOPSIS

	 use Bio::Matrix::Scoring;

DESCRIPTION

       An object which can handle AA or NT scoring matrix information.	Some transformation properties are available too.

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 the
       Bioperl mailing list.  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 of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason-at-bioperl-dot-org

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: my $obj = Bio::Matrix::Scoring->new();
	Function: Builds a new Bio::Matrix::Scoring object
	Returns : an instance of Bio::Matrix::Scoring
	Args	:

   entropy
	Title	: entropy
	Usage	: $obj->entropy($newval)
	Function:
	Example :
	Returns : value of entropy (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   expected_score
	Title	: expected_score
	Usage	: $obj->expected_score($newval)
	Function:
	Example :
	Returns : value of expected (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   scale
	Title	: scale
	Usage	: $obj->scale($newval)
	Function:
	Example :
	Returns : value of scale (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   scale_value
	Title	: scale_value
	Usage	: $obj->scale_value($newval)
	Function:
	Example :
	Returns : value of scale_value (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   description
	Title	: description
	Usage	: $obj->description($newval)
	Function:
	Example :
	Returns : value of description (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   database
	Title	: database
	Usage	: $obj->database($newval)
	Function:
	Example :
	Returns : value of database (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   lowest_score
	Title	: lowest_score
	Usage	: $obj->lowest_score($newval)
	Function:
	Example :
	Returns : value of lowest_score (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   highest_score
	Title	: highest_score
	Usage	: $obj->highest_score($newval)
	Function:
	Example :
	Returns : value of highest_score (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   lambda
	Title	: lambda
	Usage	: $obj->lambda($newval)
	Function:
	Example :
	Returns : value of lambda (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   H
	Title	: H
	Usage	: $obj->H($newval)
	Function:
	Example :
	Returns : value of H (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

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

Check Out this Related Man Page

Bio::FeatureIO::bed(3pm)				User Contributed Perl Documentation				  Bio::FeatureIO::bed(3pm)

NAME

       Bio::FeatureIO::bed - read/write features from UCSC BED format

SYNOPSIS

	 my $in = Bio::FeatureIO(-format => 'bed', -file => 'file.bed');
	 for my $feat ($in->next_feature) {
	   # do something with $feat (a Bio::SeqFeature::Annotated object)
	 }

	 my $out = Bio::FeatureIO(-format=>'bed');
	 for my $feat ($seq->get_seqFeatures) {
	   $out->write_feature($feat);
	 }

DESCRIPTION

       See <http://www.genome.ucsc.edu/goldenPath/help/customTrack.html#BED>.

       Currently for read and write only the first 6 fields (chr, start, end, name, score, strand) are supported.

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 the
       Bioperl mailing list.  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 of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Allen Day
       Email allenday@ucla.edu

CONTRIBUTORS

       Sendu Bala, bix@sendu.me.uk

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   _initialize
	Title	: _initialize
	Function: initializes BED for reading/writing
	Args	: all optional:
		  name		description
		  ----------------------------------------------------------
		  -name 	the name for the BED track, stored in header
				name defaults to localtime()
		  -description	the description for the BED track, stored in
				header.  defaults to localtime().
		  -use_score	whether or not the score attribute of
				features should be used when rendering them.
				the higher the score the darker the color.
				defaults to 0 (false)

   use_score
	Title	: use_score
	Usage	: $obj->use_score($newval)
	Function: should score be used to adjust feature color when rendering?	set to true if so.
	Example :
	Returns : value of use_score (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   name
	Title	: name
	Usage	: $obj->name($newval)
	Function: name of BED track
	Example :
	Returns : value of name (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   description
	Title	: description
	Usage	: $obj->description($newval)
	Function: description of BED track
	Example :
	Returns : value of description (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

perl v5.14.2							    2012-03-02						  Bio::FeatureIO::bed(3pm)
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