|Bio::Variation::SNP(3pm)||User Contributed Perl Documentation||Bio::Variation::SNP(3pm)|
Bio::Variation::SNP - submitted SNP
$SNP = Bio::Variation::SNP->new ();
Inherits from Bio::Variation::SeqDiff and Bio::Variation::Allele, with additional methods that are (db)SNP specific (ie, refSNP/subSNP IDs, batch IDs, validation methods).
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Usage : $is = $snp->method() Function: for getting/setting attributes Returns : a value. probably a scalar. Args : if you're trying to set an attribute, pass in the new value. Methods: -------- id type observed seq_5 seq_3 ncbi_build ncbi_chr_hits ncbi_ctg_hits ncbi_seq_loc ucsc_build ucsc_chr_hits ucsc_ctg_hits heterozygous heterozygous_SE validated genotype handle batch_id method locus_id symbol mrna protein functional_class
Title : is_subsnp Usage : $is = $snp->is_subsnp() Function: returns 1 if $snp is a subSNP Returns : 1 or undef Args : NONE
Title : subsnp Usage : $subsnp = $snp->subsnp() Function: returns the currently active subSNP of $snp Returns : Bio::Variation::SNP Args : NONE
Title : add_subsnp Usage : $subsnp = $snp->add_subsnp() Function: pushes the previous value returned by subsnp() onto a stack, accessible with each_subsnp(). Sets return value of subsnp() to a new Bio::Variation::SNP object, and returns that object. Returns : Bio::Varitiation::SNP Args : NONE
Title : each_subsnp Usage : @subsnps = $snp->each_subsnp() Function: returns a list of the subSNPs of a refSNP Returns : list Args : NONE