Bio::Polloc::LocusI - Interface of Bio::Polloc::Locus::* objects
Bio::Polloc::Locus::*
Email lmrodriguezr at gmail dot com
Bio::Polloc::Polloc::Root
Methods provided by the package
The basic initialization method
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.
Sets/gets the source genome as a Bio::Polloc::Genome object.
Bio::Polloc::Polloc::Error if unexpected type.
Sets/gets the name of the locus
Name (str), the name to set
Returns
The name (str or undef)
Gets the alias names
Aliases (arr reference or undef)
One or more alias names (str)
Gets the parent features or loci
Parents (arr reference or undef)
One or more parent object (Bio::Polloc::LocusI)
Bio::Polloc::LocusI
Bio::Polloc::Polloc::Error if some argument is not Bio::Polloc::LocusI
Gets/sets the target of the alignment, if the feature is some alignment
The ID of the target sequence
The start on the target sequence
The end on the target sequence
The strand of the target sequence
A hash reference like {id=>id, from=>from, to=>to, strand=>strand}
{id=>id, from=>from, to=>to, strand=>strand}
Gets/sets the comments on the locus, newline-separated
New comments to add (str)
Comments (str)
Gets the cross references of the locus
Array reference or undef
Adds a cross reference
One or more cross references in GFF3 format
Gets the ontology terms as explicit strings
Adds an ontology term by string
One or more strings
Gets/sets the from position
Position (int, optional)
The from position (int, -1 if undefined)
Gets/sets the to position
The to position (int, -1 if undefined)
Gets the length of the locus.
int or undef.
undef
Gets/sets the ID of the locus
ID (str)
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).
source()
The family (str, optional)
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.
Sets/gets the source of the feature. For example, the software used.
The source (str, optional).
The source (str).
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.
Gets/sets the strand
Strand (str: +, - or .)
The strand (str)
Gets/sets the origin rule
A Bio::Polloc::RuleI object
Bio::Polloc::Polloc::Error if the argument is not of the proper class
Sets/gets the score of the feature. Most loci implement different score functions, and it's often read-only.
The score (float)
Bio::Polloc::Polloc::NotImplementedException if not implemented
Sets/gets the sequence
The sequence (Bio::Seq object, optional)
The sequence (Bio::Seq object or undef)
Bio::Polloc::Polloc::Error if the sequence is not Bio::Seq
This method returns the full original sequence, not the piece of sequence with the target
Gets/sets the name of the sequence
The name of the sequence (str, optional).
The name of the sequence (str or undef).
Purpose
To provide an easy method for the (str) description of any Bio::Polloc::LocusI object.
The stringified object (str, off course)
Extracts a sequence from the context of the locus
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.
A Bio::Seq object.
Calculates the distance (referring to diversity, not genomic position) with the given locus.
The locus to compare with. Most of the locus types require this locus to be of the same type.
The reference locus. If set, replaces the loaded object as reference.
Float. The distance with the given locus. Most types will return a distance ranging from one to zero.
See the documentation for additional arguments and precisions.
Bio::Polloc::Polloc::NotImplementedException if not implemented by the correspondig class.
Methods intended to be used only within the scope of Bio::Polloc::*
Uniformizes the distinct names that every type can receive
The requested type (str)
The qualified type (str or undef)
To install Bio::Polloc, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Polloc
CPAN shell
perl -MCPAN -e shell install Bio::Polloc
For more information on module installation, please visit the detailed CPAN module installation guide.