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 listsSupport
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 : nonenumbering
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 objecteach_Variant
Title : each_Variant
Usage : $obj->each_Variant();
Function:
Returns a list of Variants.
Example :
Returns : list of Variants
Args : noneadd_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 objectSee 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 : nonedna_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 requestedSee 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