Chum::VariationTools - Tools for working on variation
Miscellaneous tools for extracting variation information and sequences
Stephen Montgomery (smontgom@bcsgc.bc.ca)
Title : get_variation_object_from_ensembl_for_name_source
Usage : my $variation = $vtools->get_variation_object_from_ensembl_for_name_source('rs999', 'dbSNP', $registry);
Function: Get a variation object from EnsEMBL
Returns : Bio::EnsEMBL::Variation::Variation object
Args : [1] String (variation name, i.e. 'rs999')
[2] String (variation source, i.e. 'dbSNP')
[3] Bio::EnsEMBL::Registry
Title : get_variation_features_for_ensembl_variation_object
Usage : my @variation_features = @{$vtools->get_variation_features_for_ensembl_variation_object($variation, $registry)};
Function: Get variation features object from EnsEMBL for a Bio::EnsEMBL::Variation::Variation object
Returns : arrayref of Bio::EnsEMBL::Variation::VariationFeature objects
Args : [1] Bio::EnsEMBL::Variation::Variation
[2] Bio::EnsEMBL::Registry
Title : get_alleles_from_seqfeatures
Usage : my @alleles = @{$vtools->get_alleles_from_seqfeatures($reference_feature, $variant_features_arrayref)};
Function: Get alleles (a String arrayref) from Bio::SeqFeature::Generic objects for reference and variants.
Each Bio::SeqFeature::Generic must have the allele, specified as an annotation called 'allele'
Returns : arrayref of String (alleles)
Args : [1] Bio::SeqFeature::Generic (reference allele annotation)
[2] arrayref of Bio::SeqFeature::Generic objects (variants allele annotation)