=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::IlluminaParser;

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

# Parser for Illumina V2 xrefs - V1 are done by the vanilla FastaParser

# Search_key,Target,ProbeId,Gid,Transcript,Accession,Symbol,Type,Start,Probe_Sequence,Definition,Ontology,Synonym
# ILMN_89282,ILMN_89282,0004760445,23525203,Hs.388528,BU678343,"",S,349,CTCTCTAAAGGGACAACAGAGTGGACAGTCAAGGAACTCCACATATTCAT,"UI-CF-EC0-abi-c-12-0-UI.s1 UI-CF-EC0 Homo sapiens cDNA clone UI-CF-EC0-abi-c-12-0-UI 3, mRNA sequence",,
# ILMN_35826,ILMN_35826,0002760372,89042416,XM_497527.2,XM_497527.2,"LOC441782",S,902,GGGGTCAAGCCCAGGTGAAATGTGGATTGGAAAAGTGCTTCCCTTGCCCC,"PREDICTED: Homo sapiens similar to spectrin domain with coiled-coils 1 (LOC441782), mRNA.",,

# Note that "definition" column often has commas.

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

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

  my @xrefs;

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

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

  while ( $_ = $file_io->getline() ) {
    chomp;

    my $xref;

    # strip ^M at end of line
    $_ =~ s/\015//g;

    my @bits = split(/,[^ ]/);
    my $illumina_id = $bits[0];
    next if ($illumina_id eq "Search_key");   # skip header
    next if (!$illumina_id); # skip lines with missing accessions

    my $sequence = $bits[9];

    my $type = $bits[7];
    # XXX what about "type" column?


    my ($description) = $bits[10];
    $description =~ s/\"//g;

    # build the xref object and store it
    $xref->{ACCESSION}     = $illumina_id;
    $xref->{LABEL}         = $illumina_id;
    $xref->{SEQUENCE}      = $sequence;
    $xref->{SOURCE_ID}     = $source_id;
    $xref->{SPECIES_ID}    = $species_id;
    $xref->{DESCRIPTION}   = $description;
    $xref->{SEQUENCE_TYPE} = 'dna';
    $xref->{STATUS}        = 'experimental';

    push @xrefs, $xref;

  }

  $file_io->close();

  $self->upload_xref_object_graphs(\@xrefs);

  print scalar(@xrefs) . " Illumina V2 xrefs succesfully parsed\n" if($verbose);


  return 0;
}

1;