Bio::Variation::SeqDiff - Container class for mutation/variant descriptions $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"; 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.

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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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email: heikki@ebi.ac.uk Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom Eckhard Lehmann, ecky@e-lehmann.de 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