Bio::Polloc::LociGroup - A group of loci
Email lmrodriguezr at gmail dot com
Bio::Polloc::Polloc::Root
Methods provided by the package
The basic initialization method
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.
Gets the 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.
Get a locus by ID
The ID of the locus (str).
Gets/sets the name of the group. This is supposed to be unique!
Future implementations could assume unique naming for getting/setting/initializing groups of loci by name.
Gets/sets the genomes to be used as analysis base.
A reference to an array of Bio::Polloc::Genome objects.
Gets/Sets the name of the feature common to all the loci in the group.
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;
Arguments work in the same way Bio::Polloc::LocusI->context_seq() arguments do.
Ref: Int, reference position.
From: Int, the from position.
To: Int, the to position.
Fixes the strand of the loci based on the flanking regions, to have all the loci in the group with the same orientation.
Context size (500 by default)
Force the detection, even if it was previously detected.
Methods intended to be used only within the scope of Bio::Polloc::*
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.