NAME
Bio::Polloc::LocusI - Interface of Bio::Polloc::Locus::* objects
AUTHOR - Luis M. Rodriguez-R
Email lmrodriguezr at gmail dot com
IMPLEMENTS OR EXTENDS
PUBLIC METHODS
Methods provided by the package
new
The basic initialization method
type
Gets/sets the type of rule
Arguments
Value (str). Can be: pattern, profile, repeat, similarity, coding. composition, crispr Some variations can be introduced, like case variations or short versions like patt or rep.
Return
Value (str). The type of the rule, or null if undefined. The value returned is undef or a string from the above list, regardless of the input variations.
Throws
Bio::Polloc::Polloc::Error if an unsupported type is received.
genome
Sets/gets the source genome as a Bio::Polloc::Genome object.
Throws
Bio::Polloc::Polloc::Error if unexpected type.
name
Sets/gets the name of the locus
Arguments
Name (str), the name to set
Returns
The name (str or undef)
aliases
Gets the alias names
Returns
Aliases (arr reference or undef)
add_alias
Arguments
One or more alias names (str)
parents
Gets the parent features or loci
Returns
Parents (arr reference or undef)
add_parent
Arguments
One or more parent object (Bio::Polloc::LocusI)
Throws
Bio::Polloc::Polloc::Error if some argument is not Bio::Polloc::LocusI
target
Gets/sets the target of the alignment, if the feature is some alignment
Arguments
- -id
-
The ID of the target sequence
- -from
-
The start on the target sequence
- -to
-
The end on the target sequence
- -strand
-
The strand of the target sequence
Returns
A hash reference like {id=>id, from=>from, to=>to, strand=>strand}
comments
Gets/sets the comments on the locus, newline-separated
Arguments
New comments to add (str)
Returns
Comments (str)
xrefs
Gets the cross references of the locus
Returns
Array reference or undef
add_xref
Adds a cross reference
Arguments
One or more cross references in GFF3 format
ontology_terms_str
Gets the ontology terms as explicit strings
Returns
Array reference or undef
add_ontology_term_str
Adds an ontology term by string
Arguments
One or more strings
from
Gets/sets the from position
Arguments
Position (int, optional)
Returns
The from position (int, -1 if undefined)
to
Gets/sets the to position
Arguments
Position (int, optional)
Returns
The to position (int, -1 if undefined)
length
Gets the length of the locus.
Returns
int or undef.
id
Gets/sets the ID of the locus
Arguments
ID (str)
Returns
ID (str)
family
Sets/gets the family of features. I.e., a name identifying the type of locus. A common family is CDS, but other families can be defined. Note that the family is not qualified by the software used for the prediction (use source() for that).
Arguments
The family (str, optional)
Returns
The family (str)
Note
This method tries to locate the family by looking (in that order) at:
The explicitly defined family.
The prefix of the ID (asuming it was produced by some Bio::Polloc::RuleI object).
The type of the rule (if the rule is defined).
If any of the former options work, returns unknown.
source
Sets/gets the source of the feature. For example, the software used.
Arguments
The source (str, optional).
Returns
The source (str).
Note
This method tries to locate the source looking (in that order) at:
The explicitly defined value.
The source of the rule (if defined).
If any of the above, returns polloc.
strand
Gets/sets the strand
Arguments
Strand (str: +, - or .)
Returns
The strand (str)
rule
Gets/sets the origin rule
Arguments
A Bio::Polloc::RuleI object
Returns
A Bio::Polloc::RuleI object
Throws
Bio::Polloc::Polloc::Error if the argument is not of the proper class
score
Sets/gets the score of the feature. Most loci implement different score functions, and it's often read-only.
Returns
The score (float)
Throws
Bio::Polloc::Polloc::NotImplementedException if not implemented
seq
Sets/gets the sequence
Arguments
The sequence (Bio::Seq object, optional)
Returns
The sequence (Bio::Seq object or undef)
Throws
Bio::Polloc::Polloc::Error if the sequence is not Bio::Seq
Note
This method returns the full original sequence, not the piece of sequence with the target
seq_name
Gets/sets the name of the sequence
Arguments
The name of the sequence (str, optional).
Returns
The name of the sequence (str or undef).
stringify
Purpose
To provide an easy method for the (str) description of any Bio::Polloc::LocusI object.
Returns
The stringified object (str, off course)
context_seq
Extracts a sequence from the context of the locus
Arguments
All the following arguments are mandatory, and must be passed in that order:
ref int : -1 to use the start as reference (useful for upstream sequences), +1 to use the end as reference (useful for downstream sequences), 0 to use the start as start reference and the end as end reference
from int : The relative start position.
to int : The relative end position.
Returns
A Bio::Seq object.
distance
Calculates the distance (referring to diversity, not genomic position) with the given locus.
Arguments
- -locus Bio::Polloc::LocusI object
-
The locus to compare with. Most of the locus types require this locus to be of the same type.
- -locusref Bio::Polloc::LocusI object
-
The reference locus. If set, replaces the loaded object as reference.
Returns
Float. The distance with the given locus. Most types will return a distance ranging from one to zero.
Note
See the documentation for additional arguments and precisions.
Throws
Bio::Polloc::Polloc::NotImplementedException if not implemented by the correspondig class.
INTERNAL METHODS
Methods intended to be used only within the scope of Bio::Polloc::*
_qualify_type
Uniformizes the distinct names that every type can receive
Arguments
The requested type (str)
Returns
The qualified type (str or undef)