#
# BioStudio functions for GFF3 interaction
#

=head1 NAME

Bio::BioStudio::GFF3 - GFF3 interaction

=head1 VERSION

Version 1.05

=head1 DESCRIPTION

BioStudio functions for GFF3

=head1 AUTHOR

Sarah Richardson <notadoctor@jhu.edu>.

=cut

package Bio::BioStudio::GFF3;

use Exporter;
use Bio::BioStudio::Basic qw($VERNAME &print_as_fasta);
use URI::Escape;
use Perl6::Slurp;
use Carp;

use strict;
use warnings;

our $VERSION = '1.05';

our @ISA = qw(Exporter);
our @EXPORT_OK = qw(
  get_GFF_comments
  make_GFF3
  gff3_string
);
our %EXPORT_TAGS = (all => \@EXPORT_OK);
 
my %PHASES = (0 => 1, 1 => 1, 2 => 1);
my $COMMENT			=	qr/^\#/;

=head1 Functions

=head2 get_GFF_comments()

Given a chromosome name and the BioStudio config hashref, returns an arrayref
containing all of the comments and directives from a GFF3 file.

=cut

sub get_GFF_comments
{
	my ($chrname, $BS) = @_;
	my ($species, $chromname) = ($1, $2) if ($chrname =~ $VERNAME);
	my $fileloc = "$BS->{genome_repository}/$species/chr$chromname/$chrname.gff";
	carp "can't find $chrname for parsing GFF comments" unless( -e $fileloc);
  my @comments = slurp $fileloc;
  @comments = grep {$_ =~ $COMMENT} @comments;
  @comments = grep {$_ !~ /^\#\#/} @comments;
	return \@comments;
}

=head2 gff3_string()

Bio::DB::SeqFeature has no gff3_out?

=cut

sub gff3_string
{
  my ($feat) = @_;
  my ($seqid, $source, $type, $start, $end, $score, $strand, $phase) =
  ($feat->seq_id(), $feat->source_tag(), $feat->primary_tag(), $feat->start(),
   $feat->end(), $feat->score(), $feat->strand(), $feat->phase());
  $score = $score ? $score  : ".";
  $phase = $phase && exists($PHASES{$phase}) ? $phase  : ".";
  $strand = $strand == "-1" ? "-" : $strand == "1"  ? "+" : ".";
  my $string = "$seqid\t$source\t$type\t$start\t$end\t$score\t$strand\t$phase\t";
  if ($feat->has_tag("load_id"))
  {
    $string .= "ID=" . $feat->Tag_load_id . ";";
    $string .= "Name=" . $feat->Tag_load_id . ";";
  }
  if ($feat->has_tag("parent_id"))
  {
    $string .= "Parent=" . $feat->Tag_parent_id . ";";
  }
  foreach my $tag (sort{$a cmp $b} $feat->get_all_tags())
  {
    next if ($tag eq "load_id" || $tag eq "parent_id");
    my @vals = $feat->get_tag_values($tag);
    if (scalar(@vals))
    {
      my $attstr = join(",", @vals);
      if ($tag eq "Note")
      {
        $string .= "$tag=" . uri_escape($attstr, '^\s^\d^\w^\-^\.^\_^\,^\(^\)') . ";";
      }
      else
      {
        $string .= "$tag=" . $attstr . ";";
      }
    }
  }
  return $string;
}

=head2 make_GFF3

=cut

sub make_GFF3
{
  my ($pa, $BS, $newcomments) = @_;
  my @NEWGFF;
 
  #comments
  my $gffheader = shift @{$pa->{COMMENTS}};
  push @NEWGFF, $gffheader, @$newcomments, @{$pa->{COMMENTS}};

  #features
  my $seq_stream = $pa->{DB}->get_seq_stream()  or die "failed to get_seq_stream()";
  my @featarr;
  while (my $seq = $seq_stream->next_seq)
  {
    push @featarr, $seq;
  }
  @featarr = sort {$a->start <=> $b->start || (($b->end - $b->start) <=> ($a->end - $a->start))} @featarr;
  push @NEWGFF, gff3_string($_) . "\n" foreach (@featarr);

  #sequence
  push @NEWGFF, @{print_as_fasta($pa->{EDITCHR}, $pa->{SEQID})};
 
	local $| = 1;
  open (OUT, ">$pa->{NEWFILE}") || die "can't open test output, $pa->{NEWFILE} $!\n";
  print OUT @NEWGFF;
	close OUT;
  return;
}

1;

__END__

=head1 COPYRIGHT AND LICENSE

Copyright (c) 2011, BioStudio developers
All rights reserved.

Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright notice, this 
list of conditions and the following disclaimer.

* Redistributions in binary form must reproduce the above copyright notice, this
list of conditions and the following disclaimer in the documentation and/or 
other materials provided with the distribution.

* Neither the name of the Johns Hopkins nor the names of the developers may be 
used to endorse or promote products derived from this software without specific 
prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
DISCLAIMED. IN NO EVENT SHALL THE DEVELOPERS BE LIABLE FOR ANY DIRECT, INDIRECT,
INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT 
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

=cut