Bio::Variation::SeqDiff(3pm)				User Contributed Perl Documentation			      Bio::Variation::SeqDiff(3pm)

NAME

       Bio::Variation::SeqDiff - Container class for mutation/variant descriptions

SYNOPSIS

	 $seqDiff = Bio::Variation::SeqDiff->new (
						  -id => $M20132,
						  -alphabet => 'rna',
						  -gene_symbol => 'AR'
						  -chromosome => 'X',
						  -numbering => 'coding'
						  );
	 # get a DNAMutation object somehow
	 $seqDiff->add_Variant($dnamut);
	 print	$seqDiff->sys_name(), "
";

DESCRIPTION

       SeqDiff stores Bio::Variation::VariantI object references and descriptive information common to all changes in a sequence. Mutations are
       understood to be any kind of sequence markers and are expected to occur in the same chromosome. See Bio::Variation::VariantI for details.

       The methods of SeqDiff are geared towards describing mutations in human genes using gene-based coordinate system where 'A' of the initiator
       codon has number 1 and the one before it -1. This is according to conventions of human genetics.

       There will be class Bio::Variation::Genotype to describe markers in different chromosomes and diploid genototypes.

       Classes implementing Bio::Variation::VariantI interface are Bio::Variation::DNAMutation, Bio::Variation::RNAChange, and
       Bio::Variation::AAChange. See Bio::Variation::VariantI, Bio::Variation::DNAMutation, Bio::Variation::RNAChange, and
       Bio::Variation::AAChange for more information.

       Variant objects can be added using two ways: an array passed to the constructor or as individual Variant objects with add_Variant method.

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 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 - Heikki Lehvaslaiho
       Email:  heikki-at-bioperl-dot-org

CONTRIBUTORS

       Eckhard Lehmann, ecky@e-lehmann.de

APPENDIX

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

   new
	 Title	 : new
	 Usage	 : $seqDiff = Bio::Variation::SeqDiff->new;
	 Function: generates a new Bio::Variation::SeqDiff
	 Returns : reference to a new object of class SeqDiff
	 Args	 :

   id
	Title	: id
	Usage	: $obj->id(H0001); $id = $obj->id();
	Function:

		  Sets or returns the id of the seqDiff.
		  Should be used to give the collection of variants a UID
		  without semantic associations.

	Example :
	Returns : value of id, a scalar
	Args	: newvalue (optional)

   sysname
	Title	: sysname
	Usage	: $obj->sysname('5C>G'); $sysname = $obj->sysname();
	Function:

		  Sets or returns the systematic name of the seqDiff.  The
		  name should follow the HUGO Mutation Database Initiative
		  approved nomenclature. If called without first setting the
		  value, will generate it from L<Bio::Variation::DNAMutation>
		  objects attached.

	Example :
	Returns : value of sysname, a scalar
	Args	: newvalue (optional)

   trivname
	Title	: trivname
	Usage	: $obj->trivname('[A2G;T56G]'); $trivname = $obj->trivname();
	Function:

		  Sets or returns the trivial name of the seqDiff.
		  The name should follow the HUGO Mutation Database Initiative
		  approved nomenclature. If called without first setting the
		  value, will generate it from L<Bio::Variation::AAChange>
		  objects attached.

	Example :
	Returns : value of trivname, a scalar
	Args	: newvalue (optional)

   chromosome
	Title	: chromosome
	Usage	: $obj->chromosome('X'); $chromosome = $obj->chromosome();
	Function:

		  Sets or returns the chromosome ("linkage group") of the seqDiff.

	Example :
	Returns : value of chromosome, a scalar
	Args	: newvalue (optional)

   gene_symbol
	Title	: gene_symbol
	Usage	: $obj->gene_symbol('FOS'); $gene_symbol = $obj->gene_symbol;
	Function:

		  Sets or returns the gene symbol for the studied CDS.

	Example :
	Returns : value of gene_symbol, a scalar
	Args	: newvalue (optional)

   description
	Title	: description
	Usage	: $obj->description('short description'); $descr = $obj->description();
	Function:

		  Sets or returns the short description of the seqDiff.

	Example :
	Returns : value of description, a scalar
	Args	: newvalue (optional)

   alphabet
	Title	: alphabet
	Usage	: if( $obj->alphabet eq 'dna' ) { /Do Something/ }
	Function: Returns the type of primary reference sequence being one of
		  'dna', 'rna' or 'protein'. This is case sensitive.

	Returns : a string either 'dna','rna','protein'.
	Args	: none

   numbering
	Title	: numbering
	Usage	: $obj->numbering('coding'); $numbering = $obj->numbering();
	Function:

		  Sets or returns the string giving the numbering schema used
		  to describe the variants.

	Example :
	Returns : value of numbering, a scalar
	Args	: newvalue (optional)

   offset
	Title	: offset
	Usage	: $obj->offset(124); $offset = $obj->offset();
	Function:

		  Sets or returns the offset from the beginning of the DNA sequence
		  to the coordinate start used to describe variants. Typically
		  the beginning of the coding region of the gene.
		  The cds_start should be 1 + offset.

	Example :
	Returns : value of offset, a scalar
	Args	: newvalue (optional)

   cds_start
	Title	: cds_start
	Usage	: $obj->cds_start(123); $cds_start = $obj->cds_start();
	Function:

		  Sets or returns the cds_start from the beginning of the DNA
		  sequence to the coordinate start used to describe
		  variants. Typically the beginning of the coding region of
		  the gene. Needs to be and is implemented as 1 + offset.

	Example :
	Returns : value of cds_start, a scalar
	Args	: newvalue (optional)

   cds_end
	Title	: cds_end
	Usage	: $obj->cds_end(321); $cds_end = $obj->cds_end();
	Function:

		  Sets or returns the position of the last nucleotitide of the
		  termination codon. The coordinate system starts from cds_start.

	Example :
	Returns : value of cds_end, a scalar
	Args	: newvalue (optional)

   rna_offset
	Title	: rna_offset
	Usage	: $obj->rna_offset(124); $rna_offset = $obj->rna_offset();
	Function:

		  Sets or returns the rna_offset from the beginning of the RNA sequence
		  to the coordinate start used to describe variants. Typically
		  the beginning of the coding region of the gene.

	Example :
	Returns : value of rna_offset, a scalar
	Args	: newvalue (optional)

   rna_id
	Title	: rna_id
	Usage	: $obj->rna_id('transcript#3'); $rna_id = $obj->rna_id();
	Function:

		   Sets or returns the ID for original RNA sequence of the seqDiff.

	Example :
	Returns : value of rna_id, a scalar
	Args	: newvalue (optional)

   add_Variant
	Title	: add_Variant
	Usage	: $obj->add_Variant($variant)
	Function:

		  Pushes one Bio::Variation::Variant into the list of variants.
		  At the same time, creates a link from the Variant to SeqDiff
		  using its SeqDiff method.

	Example :
	Returns : 1 when succeeds, 0 for failure.
	Args	: Variant object

   each_Variant
	Title	: each_Variant
	Usage	: $obj->each_Variant();
	Function:

		   Returns a list of Variants.

	Example :
	Returns : list of Variants
	Args	: none

   add_Gene
	Title	: add_Gene
	Usage	: $obj->add_Gene($gene)
	Function:

		  Pushes one L<Bio::LiveSeq::Gene> into the list of genes.

	Example :
	Returns : 1 when succeeds, 0 for failure.
	Args	: Bio::LiveSeq::Gene object

       See Bio::LiveSeq::Gene for more information.

   each_Gene
	Title	: each_Gene
	Usage	: $obj->each_Gene();
	Function:

		   Returns a list of L<Bio::LiveSeq::Gene>s.

	Example :
	Returns : list of Genes
	Args	: none

   dna_ori
	Title	: dna_ori
	Usage	: $obj->dna_ori('atgctgctgctgct'); $dna_ori = $obj->dna_ori();
	Function:

		   Sets or returns the original DNA sequence string of the seqDiff.

	Example :
	Returns : value of dna_ori, a scalar
	Args	: newvalue (optional)

   dna_mut
	Title	: dna_mut
	Usage	: $obj->dna_mut('atgctggtgctgct'); $dna_mut = $obj->dna_mut();
	Function:

		   Sets or returns the mutated DNA sequence of the seqDiff.
		   If sequence has not been set generates it from the
		   original sequence and DNA mutations.

	Example :
	Returns : value of dna_mut, a scalar
	Args	: newvalue (optional)

   rna_ori
	Title	: rna_ori
	Usage	: $obj->rna_ori('atgctgctgctgct'); $rna_ori = $obj->rna_ori();
	Function:

		   Sets or returns the original RNA sequence of the seqDiff.

	Example :
	Returns : value of rna_ori, a scalar
	Args	: newvalue (optional)

   rna_mut
	Title	: rna_mut
	Usage	: $obj->rna_mut('atgctggtgctgct'); $rna_mut = $obj->rna_mut();
	Function:

		   Sets or returns the mutated RNA sequence of the seqDiff.

	Example :
	Returns : value of rna_mut, a scalar
	Args	: newvalue (optional)

   aa_ori
	Title	: aa_ori
	Usage	: $obj->aa_ori('MAGVLL*'); $aa_ori = $obj->aa_ori();
	Function:

		   Sets or returns the original protein sequence of the seqDiff.

	Example :
	Returns : value of aa_ori, a scalar
	Args	: newvalue (optional)

   aa_mut
	Title	: aa_mut
	Usage	: $obj->aa_mut('MA*'); $aa_mut = $obj->aa_mut();
	Function:

		   Sets or returns the mutated protein sequence of the seqDiff.

	Example :
	Returns : value of aa_mut, a scalar
	Args	: newvalue (optional)

   seqobj
	Title	: seqobj
	Usage	: $dnaobj = $obj->seqobj('dna_mut');
	Function:

		   Returns the any original or mutated sequences as a
		   Bio::PrimarySeq object.

	Example :
	Returns : Bio::PrimarySeq object for the requested sequence
	Args	: string, method name for the sequence requested

       See Bio::PrimarySeq for more information.

   alignment
	Title	: alignment
	Usage	: $obj->alignment
	Function:

		  Returns a pretty RNA/AA sequence alignment from linked
		  objects.  Under construction: Only simple coding region
		  point mutations work.

	Example :
	Returns :
	Args	: none

perl v5.14.2							    2012-03-02					      Bio::Variation::SeqDiff(3pm)