=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::CeleraParser;

use strict;
use File::Basename;
use Carp;
use base qw( XrefParser::BaseParser );

# Celera database dump for anopheles - FASTA format
#
# >agCP5429,cg_name=agCG43843,ga_name=GA_x9P1GAV56A9,transcript_name=agCT42178
# MNPNSTGSSSAAGSSISTSSLPGIERLIGRENWETWKFAVQTFLELEDLWCAVKPKKNDD
# GSYESVDTAKDRKARAKIILLLEPVNYVHVKEATTAKEVWSKLEKAFDDSGLTRRVGLLH
#
# This is the parser that provides most functionality, subclasses 
# (CeleraProteinParser, CeleraTranscriptParser) just set sequence type)

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 $release_file = $ref_arg->{rel_file};
  my $verbose      = $ref_arg->{verbose};

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

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

  my $celera_gene_source_id = $self->get_source_id_for_source_name('Celera_Gene');

  my @xrefs;

  local $/ = "\n>";

  my $file_io = $self->get_filehandle($file);

  if ( !defined $file_io ) {
    print STDERR "Could not open $file\n";
    return 1;
  }

  while ( $_ = $file_io->getline() ) {
    next if (/^File:/);   # skip header

    my $xref;

    my ($header, $sequence) = $_ =~ /^>?(.+?)\n([^>]*)/s or warn("Can't parse FASTA entry: $_\n");

    # deconstruct header - just use first part
    my ($accession, $cg) = split /,/, $header;

    # make sequence into one long string
    $sequence =~ s/\n//g;

    # build the xref object and store it
    $xref->{ACCESSION}     = $accession;
    $xref->{LABEL}         = $accession;
    $xref->{SEQUENCE}      = $sequence;
    $xref->{SOURCE_ID}     = $source_id;
    $xref->{SPECIES_ID}    = $species_id;
    $xref->{SEQUENCE_TYPE} = $self->get_sequence_type();
    $xref->{STATUS}        = 'experimental';

    # pull cg_name from peptide files as well and create dependent xrefs
    if ($self->get_sequence_type() =~ /peptide/) {
      my ($cg_name) = $cg =~ /cg_name=(.*)/;
      my %dep;
      $dep{SOURCE_NAME} = 'Celera_Gene';
      $dep{LINKAGE_SOURCE_ID} = $xref->{SOURCE_ID};
      $dep{SOURCE_ID} = $celera_gene_source_id;
      $dep{ACCESSION} = $cg_name;
      push @{$xref->{DEPENDENT_XREFS}}, \%dep; # array of hashrefs
    }

    push @xrefs, $xref;

  }

  $file_io->close();


  $self->upload_xref_object_graphs(\@xrefs);
  print scalar(@xrefs) . " Celera xrefs succesfully parsed\n" if($verbose);

  return 0;
}

1;