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Genome Annotation Library - A perl toolkit for working with SO compliant genome annotations
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README.md

NAME

GAL::Annotation - Genome Annotation Library

VERSION

This document describes GAL::Annotation version 0.01

SYNOPSIS

use GAL::Annotation;

# Assuming defaults (GFF3 parser and SQLite storage)
my $annot = GAL::Annotation->new(qw(file.gff file.fasta);
my $features = $annot->features;

# Otherwise be explicit about everything.
my %feat_store_args = (class    => 'SQLite',
                       database => '/path/to/file.gff'
                      );
my $feat_store = GAL::Annotation->new(storage => \%feat_store_args,
                                      fasta   => '/path/to/file.fa');
$feat_store->load_files($feature_file);
my $features = $feat_store->schema->resultset('Feature');

# Either way, once you have features - get to work.
my $mrnas = $features->search({type => 'mRNA'});
while (my $mrna = $mrnas->next) {
  print $mrna->feature_id . "\n";
  my $CDSs = $mrna->CDSs;
  while (my $CDS = $CDSs->next) {
    print join "\n", ($CDS->start,
                      $CDS->end,
                      $CDS->seq,
                     );
  }
}

DESCRIPTION

The Genome Annotation Library (GAL) is a collection of modules that strive to make working with genome annotations simple, intuitive and fast. Users of GAL first create an annotation object which in turn will contain Parser, Storage and Schema objects. The parser allows features to be loaded into GAL's storage from a variety of formats. The storage object specifies how the features should be stored, and the schema object provides flexible query and iterator functions over the features. In addtion, Index objects (not yet implimented) provide additional key/value mapped look up tables, and List objects provide aggregation and analysis functionality for lists of feature attributes.

A wide variety of parsers are available to convert sequence features from various formats, and new parsers are easy to write. See GAL::Parser for more details. Currently SQLite and MySQL storage options are available (a fast RAM storage engine is on the TODO list). Schema objects are provided by DBIx::Class and a familiarity with that package is necessary to fully understand how to query and iterate over feature objects.

CONSTRUCTOR

New Annotation objects are created by the class method new. Arguments should be passed to the constructor as a list (or reference) of key value pairs. All attributes of the Annotation object can be set in the call to new, but reasonable defaults will be used where ever possilbe to keep object creation simple. An simple example of object creation would look like this:

my $feat_store = GAL::Annotation->new($gff_file);
my $feat_store = GAL::Annotation->new($gff_file, $fasta_file);

The resulting object would use a GFF3 parser and SQLite storage by default The first example would not have access to feature sequence, the second one would.

A more complex object creation might look like this:

my $feat_store = GAL::Annotation->new(parser  => {class => gff3},
                                      storage => {class => mysql,
                                                  dsn   => 'dbi:mysql:database'
                                                  user  => 'me',
                                                  password => 'secret'
                                      fasta   =>  '/path/to/fasta/files/'
                                      );

The constructor recognizes the following parameters which will set the appropriate attributes:

  • parser => parser_subclass [gff3]

    This optional parameter defines which parser subclass to instantiate. This parameter will default to gff3 if not provided. See GAL::Parser for a complete list of available parser classes.

  • storage => storage_subclass [SQLite]

    This optional parameter defines which storage subclass to instantiate. Currently available storage classes are SQLite (the default) and mysql.

  • fasta => '/path/to/fasta/files/

    This optional parameter defines a path to a fasta file or a collection of fasta files that correspond the annotated features. The IDs (first contiguous non-whitespace charachters) of the fasta headers must correspond to the sequence IDs (seqids) in the annotated features. The fasta parameter is optional, but if the fasta attribute is not set then the features will not have access to their sequence. Access to the sequence in provided by Bio::DB::Fasta.

new Title : new Usage : GAL::Annotation->new(); Function: Creates a GAL::Annotation object; Returns : A GAL::Annotation object Args : A list of key value pairs for the attributes specified above.

ATTRIBUTES

All attributes can be supplied as parameters to the GAL::Annotation constructor as a list (or referenece) of key value pairs.

parser Title : parser Usage : $parser = $self->parser(); Function: Create or return a parser object. Returns : A GAL::Parser::subclass object. Args : (class => gal_parser_subclass) See GAL::Parser and its subclasses for more arguments. Notes : The parser object is created as a singleton, but it can be changed by passing new arguments to a call to parser.

storage Title : storage Usage : $storage = $self->storage(); Function: Create or return a storage object. Returns : A GAL::Storage::subclass object. Args : (class => gal_storage_subclass) See GAL::Storage and its subclasses for more arguments. Notes : The storage object is created as a singleton and can not be destroyed or recreated after being created.

fasta The fasta attribute is provided by GAL::Base, see that module for more details.

METHODS

features Title : features Usage : $self->features(); Function: Return a GAL::Schema::Result::Feature object (a DBIx::Class::ResultSet for all features). Returns : A GAL::Schema::Result::Feature object Args : N/A

schema Title : schema Usage : $self->schema(); Function: Create and/or return the DBIx::Class::Schema object Returns : DBIx::Class::Schema object. Args : N/A - Arguments are provided by the GAL::Storage object.

load_files Title : load_files Usage : $a = $self->load_files(); Function: Parse and store all of the features in a file. If a single file is given as an argument and if there are gff[3] and sqlite versions of that files base name then time stamps are compared and the database is only (re)loaded if the GFF3 file is newer. Returns : N/A Args : A list of files. Notes : Default

DIAGNOSTICS

GAL::Annotation currently does not throw any warnings or errors, but most other modules in the library do, and details of those errors can be found in those modules.

CONFIGURATION AND ENVIRONMENT

GAL::Annotation requires no configuration files or environment variables.

DEPENDENCIES

Modules in GAL/lib use the following modules:

Bio::DB::Fasta Carp DBD::SQLite DBI List::Util Scalar::Util Set::IntSpan::Fast Statistics::Descriptive Text::RecordParser

Some script in GAL/bin and/or GAL/lib/GAL/t use the following modules:

Data::Dumper FileHandle Getopt::Long IO::Prompt List::MoreUtils TAP::Harness Test::More Test::Pod::Coverage URI::Escape XML::LibXML::Reader

INCOMPATIBILITIES

None reported.

BUGS AND LIMITATIONS

I'm sure there are plenty of bugs right now - please let me know if you find one.

Please report any bugs or feature requests to: barry.moore@genetics.utah.edu

AUTHOR

Barry Moore barry.moore@genetics.utah.edu

LICENCE AND COPYRIGHT

Copyright (c) 2010-2015, Barry Moore barry.moore@genetics.utah.edu. All rights reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER OF WARRANTY

BECAUSE THIS SOFTWARE IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE SOFTWARE, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE SOFTWARE "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS WITH YOU. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR, OR CORRECTION.

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE SOFTWARE AS PERMITTED BY THE ABOVE LICENCE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE SOFTWARE (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE SOFTWARE TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

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