File Coverage

blib/lib/CracTools/GFF/Annotation.pm

Criterion	Covered	Total	%
statement	76	87	87.3
branch	19	30	63.3
condition	1	3	33.3
subroutine	14	15	93.3
pod	13	13	100.0
total	123	148	83.1

###############################################################################
#                                                                             #
#    Copyright © 2012-2013 -- IRB/INSERM                                      #
#                            (Institut de Recherche en Biothérapie /          #
#                             Institut National de la Santé et de la          #
#                             Recherche Médicale)                             #
#                                                                             #
#  Auteurs/Authors:  Jerôme AUDOUX              #
#                    Nicolas PHILIPPE             #
#                                                                             #
#  -------------------------------------------------------------------------  #
#                                                                             #
#  Ce fichier fait partie de la suite CracTools qui contient plusieurs pipeline#
#  intégrés permettant de traiter les évênements biologiques présents dans du #
#  RNA-Seq. Les CracTools travaillent à partir d'un fichier SAM de CRAC et d'un#
#  fichier d'annotation au format GFF3.                                       #
#                                                                             #
#  Ce logiciel est régi  par la licence CeCILL  soumise au droit français et  #
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#  -------------------------------------------------------------------------  #
#                                                                             #
#  This file is part of the CracTools which provide several integrated        #
#  pipeline to analyze biological events present in RNA-Seq data. CracTools   #
#  work on a SAM file generated by CRAC and an annotation file in GFF3 format.#
#                                                                             #
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###############################################################################

=head1 NAME

CracTools::GFF::Annotation - Parse GFF lines.

=head1 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->attribute('gene_id'),"\n";
  }

=head1 DESCRIPTION

CracTools::GFF::Annotataion is an object to parse and access GFF line's fields.

=cut

package CracTools::GFF::Annotation;

use Carp;

=head1 METHODS

=head2 new

  Arg [1] : String - $line
            GFF line
  Arg [2] : String - $format (optional) - default 'gff2'
            GFF format (gff2 or gff3)

  Example     : my $annotation = CracTools::GFF::Annotation->new($gff_line);
  Description : Create a new CracTools::GFF::Annotation object
                If a gff line is passed in argument, the line will be parsed
                and loaded.
  ReturnType  : CracTools::GFF::Query
  Exceptions  : none

=cut

sub new {
  my $class = shift;
  my $line = shift;
  my $format = shift;
  if(!defined $format) {
    $format = 'gff2';
  }

  my $self = bless {format => $format}, $class;

  if(defined $line) {
    $self->_init($line);
  }

  return $self;
}

sub _init {
  my ($self,$line) = @_;

  # Split the line with TABS
  my ($chr,$source,$feature,$start,$end,$score,$strand,$phase,$attributes) = split("\t",$line);

  # Get the strand if 1/-1 format
  $strand = convertStrand($strand);

  # Loading the 8 first columns
  $self->{chr} = $chr;
  $self->{source} = $source;
  $self->{feature} = $feature;

  # Conversion to 0-based coordinate system
  $self->{start} = $start-1;
  $self->{end} = $end-1;

  $self->{score} = $score;
  $self->{strand} = $strand;
  $self->{phase} = $phase;

  # Loading attributes
  my @attributes_tab = split(";",$attributes);
  foreach my $attr (@attributes_tab) {
    my ($k,$v);
    if($self->{format} =~ /gff3/i) {
      ($k,$v) = $attr =~ /(\S+)=(.*)/;
    } else {
      ($k,$v) = $attr =~ /(\S+)\s+"(.*)"/;
    }
    if(defined $k && defined $v) {
      $self->{attributes}{$k} = $v;
    } #else {
    #  carp("Error parsing attribute $attr");
    #}
  }

}

=head1 GETTERS AND SETTERS

=head2 chr

  Description : Getter/setter for attribute chr

=cut

sub chr {
  my $self = shift;
  my $chr = shift;
  if(defined $chr) {
    $self->{chr} = $chr;
  }
  return $self->{chr};
}

=head2 source

  Description : Getter/setter for attribute source

=cut

sub source {
  my $self = shift;
  my $source = shift;
  if(defined $source) {
    $self->{source} = $source;
  }
  return $self->{source};
}

=head2 feature

  Description : Getter/setter for attribute feature

=cut

sub feature {
  my $self = shift;
  my $feature = shift;
  if(defined $feature) {
    $self->{feature} = $feature;
  }
  return $self->{feature};
}

=head2 start

  Description : Getter/setter for attribute start

=cut

sub start {
  my $self = shift;
  my $start = shift;
  if(defined $start) {
    $self->{start} = $start;
  }
  return $self->{start};
}

=head2 end

  Description : Getter/setter for attribute end

=cut

sub end {
  my $self = shift;
  my $end = shift;
  if(defined $end) {
    $self->{end} = $end;
  }
  return $self->{end};
}

=head2 score

  Description : Getter/setter for attribute score

=cut

sub score {
  my $self = shift;
  my $score = shift;
  if(defined $score) {
    $self->{score} = $score;
  }
  return $self->{score};
}

=head2 strand

  Description : Getter/setter for attribute strand ('+','-' convention)

=cut

sub strand {
  my $self = shift;
  my $strand = shift;
  if(defined $strand) {
    $self->{strand} = $strand;
  }
  return $self->{strand};
}

=head2 gffStrand

  Description : Return strand using "1","-1" convention.

=cut

sub gffStrand {
  my $self = shift;
  return convertStrand($self->{strand});
}

=head2 phase

  Description : Getter/setter for attribute phase

=cut

sub phase {
  my $self = shift;
  my $phase = shift;
  if(defined $phase) {
    $self->{phase} = $phase;
  }
  return $self->{phase};
}

=head2 parents

  Description : Getter for attribute parents.
  ReturnType  : Array of strings with parents ID

=cut

sub parents {
  my $self = shift;
  if(defined $self->attribute('Parent')) {
    return split(',',$self->attribute('Parent'));
  } else {
    return ();
  }
}

=head2 attribute

  Description : Getter/setter for attribute attribute

=cut

sub attribute {
  my $self = shift;
  my $key = shift;
  my $value = shift;
  if(defined $value) {
    return $self->{attributes}{$key} = $value;
  } elsif(defined $key) {
    return $self->{attributes}{$key};
  } else {
    return undef;
    #croak ("Missing attribute key to retreive attribute value");
  }
}

=head1 STATIC METHODS

=head2 convertStrand

  Arg [1] : Character - strand using '+' and '-' signs

  Description : Retrun the strand using the (1,-1) convention
                instead of the ('+','-') convention of GFF files.
=cut

sub convertStrand($) {
  my $strand = shift;
  my %conversion_hash = ( '+' => 1, '-' => -1, 1 => '+', -1 => '-');
  return $conversion_hash{$strand};
}

1;