NAME

GenOO - A Modern Perl Framework for High Throughput Sequencing analysis

SYNOPSIS

GenOO [jee-noo] is an object-oriented framework developed for the analysis of High Throughput Sequencing (HTS) data.
The primary aim of GenOO is to make simple HTS analyses easy and complicated analyses possible.

DESCRIPTION

GenOO models biological entities into objects and provides methods for the manipulation of high throughput
sequencing data. Using GenOO as a core development module reduces the overhead and complexity of managing
the data and the biological entities at hand. GenOO has been designed to be flexible, easily extendable with modular
structure and minimal requirements for external tools and libraries.

Source code: The source has been deposited in GitHub L<https://github.com/genoo/GenOO>.

Documentation: A cookbook with basic ideas and examples is available in GitHub L<https://github.com/genoo/GenOO/tree/master/cookbook>

Contribute: Please fork the GitHub repository and provide patches, features or tests.

Bugs: Please open issues in the GitHub repository

EXAMPLES

####################
# Parse a BED file. Similar for SAM, Fasta, FastQ etc.
my $bed_parser = GenOO::Data::File::BED->new(
    file => 'input_file.bed'
);
while (my $record = $file_parser->next_record) {
    # $record is an instance of GenOO::Data::File::BED::Record
    print $record->name."\n"; # name
    print $record->strand."\n"; # strand
    print $record->length."\n"; # length
    print $record->head_position."\n"; # genomic location of the 5'end of the read
    print $record->to_string."\n"; # prints the record back in BED format
}

####################
# Create gene models from a GTF file
my $transcript_collection = GenOO::TranscriptCollection::Factory->create('GTF', {
    file => 'transcripts_file.gtf'
})->read_collection;

# The gene models are now in a region collection type object
# Loop on the collection and execute some code for each transcript
$transcript_collection->foreach_record_do(sub{
    my ($transcript) = @_;
    
    print $transcript->id."\n" if $transcript->is_coding;
    # more code
});

####################
# Remember the BED parser before? Now instead of parsing the file line by line we
# want to add its entries in a collection so we can perform range queries on it.
my $reads_collection = GenOO::RegionCollection::Factory->create('BED', {
    file => 'input_file.bed'
})->read_collection;

# Get the reads of the BED file that overlap with a specified region
my @overlapping_reads = $reads_collection->records_overlapping_region($strand, $chromosome, $start, $stop)

# Any collection can be used to perform range queries on it, including the transcript collection above.

...
# For more information and examples check the cookbook in L<https://github.com/genoo/GenOO/tree/master/cookbook>