Chum::Stackbuilder - Builds a stack of orthologous sequences around a source of variation
Builds a stack of orthologous sequences around a source of variation
Stephen Montgomery (smontgom@bcsgc.bc.ca)
Function: Instantiates a Stackbuilder
Usage : my $stackbuilder = new Stackbuilder(); or
my $stackbuilder = new Stackbuilder( '_memconserve' => 1, ##Conserve memory by reducing embedded object sizes (optional)
'_registry' => "Bio::EnsEMBL::Registry", ##The EnsEMBL Registry for fetching orthologues (optional)
'_upstream' => 100, ##The upstream sequence to fetch around a variant (optional)
'_downstream' => 100, ##The downstream sequence to fetch around a variant (optional)
'_species' => $species_arrayref, ##The species to get orthologues for (optional)
'_binomials' => $binomials_hashref); ##Hashref of species binomial names (optional)
Returns : Chum::Stackbuilder
Function: Gets a Chum::Stack object for a variation name and source database (recognized by EnsEMBL)
Usage : $stackbuilder->generate_stack_from_variation_name_source('rs999', 'dbSNP');
Throws : Exception if the variation object cannot be uniquely mapped to the genome
Returns : Chum::Stack
Args : [1] String (variation_name, i.e. rs999)
[2] String (variation_source, i.e. dbSNP)
Function: Gets a Chum::Stack object for a variation_feature object Usage : $stackbuilder->generate_stack_from_variation_feature_object($variation_feature); Returns : Chum::Stack Args : [1] Bio::EnsEMBL::Variation::VariationFeature
Function: From a specially formatted GFF file, assemble Chum::Stack objects
Usage : $stackbuilder->generate_stacks_from_variation_file('variation.gff');
The variation GFF file must be in the format
VARIANT-1 CHROMOSOME VARIANTID 100000 100001 . + . T
REFERENCE-1 CHROMOSOME VARIANTID 100000 100001 . + . C
VARIANT-2 CHROMOSOME VARIANTID 200000 200001 . + . -
VARIANT-2 CHROMOSOME VARIANTID 200000 200001 . + . A
REFERENCE-2 CHROMOSOME VARIANTID 200000 200001 . + . G
etc...
Returns : arrayref of Chum::Stack objects
Args : String (filename) of variation GFF file.
Title : _generate_stack_for_variation_feature
Usage : my $stack = $stackbuilder->_generate_stack_for_variation_feature($variation_feature, $binomial_hashref, $method);
Function: For an EnsEMBL VariationFeature, generate a Chum::Stack object
Returns : a Chum::Stack object
Args : [1] Bio::EnsEMBL::Variation::VariationFeature
[2] hashref (species binomial)
[3] method (String, optional - what method to use in compara for obtaining orthologous sequences)
Title : _generate_stack_for_seqfeature
Usage : my $stack = $stackbuilder->_generate_stack_for_seqfeature($reference_feature, $variation_features_arrayref, $binomial_hashref, $method);
Function: For Bio::SeqFeature::Generic (reference object and variants arrayref), generate a Chum::Stack object
Returns : a Chum::Stack object
Args : [1] Bio::SeqFeature::Generic (reference allele feature)
[2] arrayref (Bio::SeqFeature::Generic variant allele features)
[3] hashref (binomial species names)
[3] method (String, optional - what method to use in compara for obtaining orthologous sequences)
Title : _get_slice_for_variation_feature Usage : my $slice = $stackbuilder->_get_slice_for_variation_feature($variation_feature); Function: For an EnsEMBL VariationFeature, get a surrounding genomic slice Returns : a Bio::EnsEMBL::Slice feature Args : [1] Bio::EnsEMBL::Variation::VariationFeature
Title : _get_slice_for_seqfeature Usage : my $slice = $stackbuilder->_get_slice_for_seqfeature($sequence_feature); Function: For an Bio::SeqFeature::Generic, get a surrounding genomic slice Returns : a Bio::EnsEMBL::Slice feature Args : [1] Bio::SeqFeature::Generic object
Title : _get_orthologous_sequences_for_slice
Usage : my @sequences = @{$stackbuilder->_get_orthologous_sequences_for_slice($slice, $binomialhashref, 'BLASTZ_NET')};
Function: For an EnsEMBL Slice, get all the orthologous sequences defined in the compara database for a particular method.
Returns : an arrayref of Bio::LocatableSeq objects
Args : [1] Bio::EnsEMBL::Slice
[2] hashref (species binomials)
[3] String (method, optional)
Title : _get_species_binomials Usage : my $binomial_hashref = $stackbuilder->_get_species_binomials(); Function: Obtain all the binomial species names from EnsEMBL Compara database Returns : an hashref of Strings (species binomial names) Args : none