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