Luis M Rodríguez-R
and 1 contributors

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

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

5 POD Errors

The following errors were encountered while parsing the POD:

Around line 44:

Expected '=item *'

Around line 77:

Expected '=item *'

Around line 137:

Expected '=item *'

Around line 164:

Expected '=item *'

Around line 168:

Expected '=item *'