Bio::Variation::SeqDiff(3)

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