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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(), "\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:

   http://bugzilla.open-bio.org/
 
 

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