=head1 LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2019] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=cut

package XrefParser::VbGFF3Parser;

use strict;
use warnings;
use Carp;
use File::Basename;
use Bio::SeqIO;

# perl xref_parser.pl -user ensadmin -pass PASS -host genebuild2 -dbname snr_anopheles_gambiae_48_xref_test -species anopheles_gambiae -source ARRAY_JHSPH_AGGAMBER_15k_v1 -download_path $mywork/VB_xref/downloads/ -checkdownload


use base qw( XrefParser::CoordinateParser );

# Parser for GFF3-format probe mappings from Vectorbase
sub run {

  my ($self, $ref_arg) = @_;
  my $source_id    = $ref_arg->{source_id};
  my $species_id   = $ref_arg->{species_id};
  my $files        = $ref_arg->{files};
  my $verbose      = $ref_arg->{verbose};

  if((!defined $source_id) or (!defined $species_id) or (!defined $files) ){
    croak "Need to pass source_id, species_id and files as pairs";
  }
  $verbose |=0;

  my $file = @{$files}[0];

  open (my $FH, "<", $file) || return 1;
  my $i=0; my $type = "transcript";
  while (my $ln = <$FH>) {
#	# parse GFF line:
    chomp($ln); $i++;
    my ($seqid, $source, $type, $start, $end, $score, $strand, $phase, $attributes) = split("\t",$ln);
    if ($strand eq "."){
      $strand = 0;
    }
    elsif ($strand eq "?"){
      $strand = 0;
    }# nb should more properly be NULL;
    my %attributes;
    unless ($attributes eq ".") {
      my @attributes = split(";",$attributes);
      foreach my $pair ( @attributes ){
	my ($key, $value) = split("=",$pair);
	
	if ($value =~ m/,/i ) {
	  my @values = split(",",$value);
	  foreach my $splitval (@values) {
	    $splitval =~ s/%59/;/;
	    $splitval =~ s/%44/,/;
	    $splitval =~ s/%61/=/;
	    push (@{$attributes{uc($key)}},$splitval);
	  }
	}
	else {
	  $value =~ s/%59/;/;
	  $value =~ s/%44/,/;
	  $value =~ s/%61/=/;
	  push(@{$attributes{uc($key)}},$value);
	}
      }
    }


    #		# assess and build oligo_feature
    if (($seqid eq ".") || ($start eq ".") || ($end eq ".")) {
      #				_parse_error(\%attributes,"incomplete location (".$seqid.":".$start."-".$end.")");
    }
    else {
      foreach my $name (@{$attributes{"NAME"}}) {
	my %xref = ( 'accession'  => $name,
		     'chromosome' => $seqid,
		     'strand'     => $strand,
		     'txStart'    => $start,
		     'txEnd'      => $end,
		     'cdsStart'   => $start,
		     'cdsEnd'     => $end,
		     'exonStarts' => $start,
		     'exonEnds'   => $end );
	print STDERR "$name, $start, $end\n" if($verbose);
	$self->add_xref( $source_id, $species_id, \%xref );
      }
    }
  }
  print STDERR $i." VB GFF3 xrefs succesfully parsed\n" if($verbose);
  close($FH);

  return 0;
} ## end sub run

1;