Provided by: libbio-perl-perl_1.7.2-3_all bug

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(), "\n";

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://github.com/bioperl/bioperl-live/issues

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