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Luis M Rodríguez-R > Polloc-1.5.3b > Bio::Polloc::LociGroup

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Module Version: 1.0503   Source  

NAME ^

Bio::Polloc::LociGroup - A group of loci

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

add_locus

Alias of add_loci()

add_loci

Adds loci to the collection on the specified genome's space

Throws

A Bio::Polloc::Polloc::Error if an argument is not a Bio::Polloc::LocusI object.

Arguments

The first argument can be the identifier of the genome's space (int). All the following are expected to be Bio::Polloc::LocusI objects.

loci

Gets the loci

structured_loci

Returns a two-dimensional array where the first key corresponds to the number of the genome space and the second key is an incremental for each locus.

Note

This function is provided for convenience in some output formating, but its use should be avoided as it causes a huge processing time penalty.

Warning

Loci without defined genome will not be included in the output.

locus

Get a locus by ID

Arguments

The ID of the locus (str).

name

Gets/sets the name of the group. This is supposed to be unique!

Note

Future implementations could assume unique naming for getting/setting/initializing groups of loci by name.

genomes

Gets/sets the genomes to be used as analysis base.

Arguments

A reference to an array of Bio::Polloc::Genome objects.

featurename

Gets/Sets the name of the feature common to all the loci in the group.

avg_length

Gets the average length of the stored loci.

Returns

The average length (float) or an array containing the average length (float) and the standard deviation (float), depending on the expected output.

Syntax

    my $len = $locigroup->length;

Or,

    my($len, $sd) = $locigroup->length;

align_context

Arguments

Arguments work in the same way Bio::Polloc::LocusI->context_seq() arguments do.

  1. Ref: Int, reference position.
  2. From: Int, the from position.
  3. To: Int, the to position.

fix_strands

Fixes the strand of the loci based on the flanking regions, to have all the loci in the group with the same orientation.

Arguments

-size int

Context size (500 by default)

-force bool (int)

Force the detection, even if it was previously detected.

INTERNAL METHODS ^

Methods intended to be used only within the scope of Bio::Polloc::*

_initialize

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