ensembl-hive
2.6
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A Slice object represents a region of a genome. It can be used to retrieve sequence or features from an area of interest.
Definition at line 48 of file CircularSlice.pm.
protected Bio::EnsEMBL::CircularSlice::_split | ( | ) |
Undocumented method
public Bio::EnsEMBL::CircularSlice::accession_number | ( | ) |
Description: Included for Bio::PrimarySeqI interface compliance (1.2)
public Bio::EnsEMBL::CircularSlice::alphabet | ( | ) |
Description: Included for Bio::PrimarySeqI interface compliance (1.2)
public Int Bio::EnsEMBL::CircularSlice::centrepoint | ( | ) |
Arg [1] : none Example :
Description: Returns the mid position of this slice relative to the start of the sequence region that it was created on. Coordinates are inclusive and start at 1. Returntype : int Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::CircularSlice::desc | ( | ) |
Description: Included for Bio::PrimarySeqI interface compliance (1.2)
public Bio::EnsEMBL::CircularSlice::display_id | ( | ) |
Description: Included for Bio::PrimarySeqI interface compliance (1.2)
public Bio::EnsEMBL::Slice Bio::EnsEMBL::CircularSlice::expand | ( | ) |
Arg [1] : (optional) int $five_prime_expand The number of basepairs to shift this slices five_prime coordinate by. Positive values make the slice larger, negative make the slice smaller. coordinate left. Default = 0. Arg [2] : (optional) int $three_prime_expand The number of basepairs to shift this slices three_prime coordinate by. Positive values make the slice larger, negative make the slice smaller. Default = 0. Arg [3] : (optional) bool $force_expand if set to 1, then the slice will be contracted even in the case when shifts $five_prime_expand and $three_prime_expand overlap. In that case $five_prime_expand and $three_prime_expand will be set to a maximum possible number and that will result in the slice which would have only 2pbs. Default = 0. Arg [4] : (optional) int* $fpref The reference to a number of basepairs to shift this slices five_prime coordinate by. Normally it would be set to $five_prime_expand. But in case when $five_prime_expand shift can not be applied and $force_expand is set to 1, then $$fpref will contain the maximum possible shift Arg [5] : (optional) int* $tpref The reference to a number of basepairs to shift this slices three_prime coordinate by. Normally it would be set to $three_prime_expand. But in case when $five_prime_expand shift can not be applied and $force_expand is set to 1, then $$tpref will contain the maximum possible shift Example :
Description: Returns a slice which is a resized copy of this slice. The start and end are moved outwards from the center of the slice if positive values are provided and moved inwards if negative values are provided. This slice remains unchanged. A slice may not be contracted below 1bp but may grow to be arbitrarily large. Returntype : Bio::EnsEMBL::Slice Exceptions : warning if an attempt is made to contract the slice below 1bp Caller : general Status : Stable
public Hashref Bio::EnsEMBL::CircularSlice::get_all_DASFeatures | ( | ) |
Arg [1] : none Example :
Description: Retrieves a hash reference to a hash of DAS feature sets, keyed by the DNS, NOTE the values of this hash are an anonymous array containing: (1) a pointer to an array of features; (2) a pointer to the DAS stylesheet Returntype : hashref of Bio::SeqFeatures Exceptions : ? Caller : webcode Status : Stable
public Listref Bio::EnsEMBL::CircularSlice::get_all_genotyped_VariationFeatures | ( | ) |
Args : none Description: returns all variation features on this slice that have been genotyped. This function will only work correctly if the variation database has been attached to the core database. ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature Exceptions : none Caller : contigview, snpview, ldview Status : At Risk : Variation database is under development.
public Listref Bio::EnsEMBL::CircularSlice::get_all_VariationFeatures | ( | ) |
Args : $filter [optional] Description:returns all variation features on this slice. This function will only work correctly if the variation database has been attached to the core database. If $filter is "genotyped" return genotyped Snps only... (nice likkle hack); ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature Exceptions : none Caller : contigview, snpview Status : At Risk : Variation database is under development.
public Bio::EnsEMBL::CircularSlice::id | ( | ) |
Description: Included for Bio::PrimarySeqI interface compliance (0.7)
public Bio::EnsEMBL::CircularSlice::is_circular | ( | ) |
Description: Included for Bio::PrimarySeqI interface compliance (1.2)
public Int Bio::EnsEMBL::CircularSlice::length | ( | ) |
Arg [1] : none Example :
Description: Returns the length of this slice in basepairs Returntype : int Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::CircularSlice::moltype | ( | ) |
Description: Included for Bio::PrimarySeqI interface compliance (0.7)
public Bio::EnsEMBL::CircularSlice Bio::EnsEMBL::CircularSlice::new | ( | ) |
Arg [...] : List of named arguments Bio::EnsEMBL::CoordSystem COORD_SYSTEM string SEQ_REGION_NAME, int START, int END, int SEQ_REGION_LENGTH, (optional) string SEQ (optional) int STRAND, (optional, defaults to 1) Bio::EnsEMBL::DBSQL::SliceAdaptor ADAPTOR (optional) Example :
Description: Creates a new slice object. A slice represents a region of sequence in a particular coordinate system. Slices can be used to retrieve sequence and features from an area of interest in a genome.
Coordinates start at 1 and are inclusive. Negative coordinates or coordinates exceeding the length of the seq_region are permitted. Start must be less than or equal. to end regardless of the strand.
Slice objects are immutable. Once instantiated their attributes (with the exception of the adaptor) may not be altered. To change the attributes a new slice must be created.
Returntype : Bio::EnsEMBL::CircularSlice Exceptions : throws if start, end, coordsystem or seq_region_name not specified or not of the correct type Caller : general, Bio::EnsEMBL::SliceAdaptor Status : Stable
public Bio::EnsEMBL::CircularSlice::primary_id | ( | ) |
Description: Included for Bio::PrimarySeqI interface compliance (1.2)
public List Bio::EnsEMBL::CircularSlice::project_to_slice | ( | ) |
Arg [1] : Slice to project to. Example :
$chr_slice->strand(). " length: ".($chr_slice->end()-$chr_slice->start()+1). "\n"; } Description: Projection of slice to another specific slice. Needed for where we have multiple mappings and we want to state which one to project to. Returntype : list reference of Bio::EnsEMBL::ProjectionSegment objects which can also be used as [$start,$end,$slice] triplets. Exceptions : none Caller : none Status : At Risk
public String Bio::EnsEMBL::CircularSlice::seq | ( | ) |
Arg [1] : none Example :
Description: Returns the sequence of the region represented by this slice formatted as a string. Returntype : string Exceptions : none Caller : general Status : Stable
public Txt Bio::EnsEMBL::CircularSlice::subseq | ( | ) |
Arg [1] : int $startBasePair relative to start of slice, which is 1. Arg [2] : int $endBasePair relative to start of slice. Arg [3] : (optional) int $strand The strand of the slice to obtain sequence from. Default value is 1. Description: returns string of dna sequence Returntype : txt Exceptions : end should be at least as big as start strand must be set Caller : general Status : Stable