NAME
CracTools::GFF::Query - Query GFF files easily.
SYNOPSIS
Usage:
use CracTools::GFF::Query;
# Creating the reader
my $gffQuery = CracTools::GFF::Query->new('annotations.gff');
my @annotations = $gffQuery->fetchByLocation('1',298345,'+');
foreach my $gff_line (@annotations) {
my $annotation = CracTools::GFF::Annotation->new($gff_line);
print "Gene_id : ",$annotation->getAttribute('gene_id'),"\n";
}
DESCRIPTION
CracTools::GFF::Query is a tool to query GFF files without building a database.
It is memory efficient and designed to run fast.
You can easily retrives GFF data from a specific region of position.
This tool can be use with CracTools::GFF::Annotation in order to parse GFF line
into a nice usable Perl Object.
METHODS
new
Arg [1] : String - GFF file
Example : my $gffQuery = CracTools::GFF::Query->new('annotations.gff');
Description : Create a new GFF Query object
ReturnType : CracTools::GFF::Query
Exceptions : none
fetchByRegion
Arg [1] : String $seq_region_name
The name of the sequence region that the slice will be
created on.
Arg [2] : int $start
The start of the slice on the sequence region
Arg [3] : int $end
The end of the slice on the sequence region
Arg [4] : int $strand
The orientation of the slice on the sequence region
Example : my @annotations = $gffQuery->fetchByRegion('1',298345,309209,'+');
Description : Retrives GFF lines that belong to the region.
ReturnType : Reference to an Array of strings
Exceptions : none
fetchByLocation
Arg [1] : String $seq_region_name
The name of the sequence region that the slice will be
created on.
Arg [2] : int $position
Location to look for
Arg [3] : int $strand
The orientation of the slice on the sequence region
Example : my @annotations = $gffQuery->fetchByLocation('1',298345,'+');
Description : Retrives GFF lines that belong to the location.
ReturnType : Reference to an Array of strings
Exceptions : none