NAME

Bio::Polloc::Genome - A group of sequences from the same organism

AUTHOR - Luis M. Rodriguez-R

Email lmrodriguezr at gmail dot com

LICENSE

This package is licensed under the Artistic License - see LICENSE.txt

IMPLEMENTS OR EXTENDS

• Bio::Polloc::Polloc::Root

PUBLIC METHODS

Methods provided by the package

new

• The basic initialization method

• Arguments

  -name str

  The name of the genome (from file if not provided).

  -file str

  The file containing the (multi-)fasta with the genome.

build_set

• Builds a set of genomes.

• Arguments

  -files arrayref

  An arrayref containing the files from which genomes must be build.

  -names arrayref

  An arrayref containing the names of the genomes (in the same order of the files).

file

• Sets/gets the file containing the genome

get_sequences

• Gets the collection of sequences.

• Returns

  An array of Bio::Seq objects.

search_sequence

• Search a sequence by ID

• Arguments

  The id (str) of the sequence.

• Returns

  The sequence (Bio::Seq) or undef.

name

• Gets/sets the name of the genome. If no name is set, tries to use the file instead.

INTERNAL METHODS

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

_initialize