Chum::Stack - An analysis stack object
A set of orthologous sequences, and reference and variant sequences with their associated alleles inserted. An option variation_ref_obj parameter provides metadata about the stack. It can be either a string or a Bio::EnsEMBL::Variation::VariationFeature object
Example:
my $stack = new Chum::Stack( 'reference_sequence' => $reference_sequence, ##A Chum::VariantSequence object 'orthologous_sequences' => \@orthologous_sequences, ##An arrayref of Bio::Seq or Bio::LocatableSeq objects 'variant_sequences' => \@variant_sequences, ##An arrayref of Chum::VariantSequence objects 'variant_ref_obj' => $variation_feature);
The essential difference between the reference sequence and the variant sequence is that the reference sequence is located in a canonical genome assembly. The stack object can be used to test various sequence combinations for allele specific results. For instance as input to an analysis program, the reference sequence will be run against various variant_sequences to determine the effects an allele has on the results of a particular analysis.
The easiest way of creating new Chum::Stack objects is through the Chum::Utils::RSNPAnalysisXMLFileReader They can also be created by direct calls to EnsEMBL or from appropriately formatted GFF files (which can gather sequence from EnsEMBL).
Stephen Montgomery (smontgom@bcsgc.bc.ca)
Usage : $stack->reference_sequence;
the variant sequence that is present in a canonical genome assembly (i.e. human), it is not
present in the orthologous sequences array and should be added when performing tasks
such as "phylogenetic footprinting"
Returns : Chum::VariantSequence
Args : none
Usage : my @orthologous_sequences = @{$stack->orthologous_sequences};
sequences identified as orthologous to the reference sequence
Returns : an arrayref of Bio::Seq or Bio::LocatableSeq objects
Args : none
Usage : my @variant_sequences = @{$stack->variant_sequences};
sequences with variant alleles inserted, typically not in a canonical genome assembly
Returns : an arrayref of Chum::VariantSequence objects
Args : none
Usage : $stack->variation_ref_obj;
An optional meta data object containing information on the variation this stack object is
associated to.
Returns : string or a Bio::EnsEMBL::Variation::VariationFeature
Args : none
Usage : $stack->get_variation_name;
The name of the variant, i.e. "rs1234567" (dbSNP)
Returns : string
Args : none
Usage : my @ids = @{$stack->get_orthologous_sequence_ids};
The display ids of the orthologous sequences.
Returns : an arrayref of strings
Args : none
Usage : my $chimp_seq_obj = $stack->get_orthologous_sequence_by_id("patr");
T
Returns : A Bio::Seq or Bio::LocatableSeq object
Args : arg1: the id of the orthologous sequence to return
Usage : $stack->get_sequence_ids_string
The display ids of the sequences with their sequence lengths
Simple way of outputting a stacks contents to the display.
Returns : string
Args : none