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NAME

Chum::Stack - An analysis stack object

SYNOPSIS

DESCRIPTION

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).

CONTACT

Stephen Montgomery (smontgom@bcsgc.bc.ca)

METHODS

reference_sequence

 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

orthologous_sequences

 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

variant_sequences

 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

variation_ref_obj

 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

get_variation_name

 Usage   : $stack->get_variation_name;
                   The name of the variant, i.e. "rs1234567" (dbSNP)
 Returns : string
 Args    : none

get_orthologous_sequence_ids

 Usage   : my @ids = @{$stack->get_orthologous_sequence_ids};
                   The display ids of the orthologous sequences.
 Returns : an arrayref of strings
 Args    : none

get_orthologous_sequence_by_id

 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

get_sequence_ids_string

 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

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