lib/CXGN/BrAPI/v2/Variants.pm

   1 package CXGN::BrAPI::v2::Variants;
   2
   3 use Moose;
   4 use Data::Dumper;
   5 use SGN::Model::Cvterm;
   6 use CXGN::Marker::SearchBrAPI;
   7 use CXGN::BrAPI::FileResponse;
   8 use CXGN::BrAPI::Pagination;
   9 use CXGN::BrAPI::JSONResponse;
  10 use JSON;
  11
  12 use CXGN::DB::Connection;
  13
  14 extends 'CXGN::BrAPI::v2::Common';
  15
  16 sub search {
  17     my $self = shift;
  18     my $inputs = shift;
  19     my $page_size = $self->page_size;
  20     my $page = $self->page;
  21     my $status = $self->status;
  22
  23     my $marker_ids = $inputs->{variantDbId}  || ($inputs->{variantDbIds} || []);
  24     my $variantset_ids = $inputs->{variantSetDbId}  || ($inputs->{variantSetDbIds} || []);
  25     my @callset_ids = $inputs->{callSetDbIds} ? @{$inputs->{callSetDbIds}} : ();
  26     my $start = $inputs->{start}->[0] || undef;
  27     my $end = $inputs->{end}->[0] || undef;
  28     my $pageToken = $inputs->{pageToken}->[0] || undef;
  29     my $schema = $self->bcs_schema;
  30     my @data_out;
  31
  32     if (@callset_ids && scalar(@callset_ids)>0){
  33         push @$status, { 'error' => 'The following search parameters are not implemented: callSetDbIds' };
  34     }
  35
  36     my @trial_ids =();
  37     my @protocol_ids = ();
  38     if ( $variantset_ids){
  39         foreach ( @{$variantset_ids} ){
  40             my @ids = split /p/, $_;
  41             push @trial_ids, $ids[0] ? $ids[0] : ();
  42             push @protocol_ids, $ids[1] ? $ids[1] : ();
  43         }
  44     }
  45
  46     my $marker_search = CXGN::Marker::SearchBrAPI->new({
  47         bcs_schema => $schema,
  48         protocol_id_list => \@protocol_ids,
  49         project_id_list => \@trial_ids,
  50         marker_name_list => $marker_ids,
  51         #protocolprop_marker_hash_select=>['name', 'chrom', 'pos', 'alt', 'ref'] Use default which is all marker info
  52         offset=>$page_size*$page,
  53         limit=>$page_size
  54     });
  55
  56     my $start_index = $page*$page_size;
  57     my $end_index = $page*$page_size + $page_size - 1;
  58     my $counter = 0;
  59
  60     my ($data, $total_count) = $marker_search->search();
  61
  62     foreach (@$data){
  63         if ($counter >= $start_index && $counter <= $end_index) {
  64             my $info = $_->{info};
  65             my $svtype = $1 if ($_->{info} =~ /SVTYPE=(\w+);/) ;
  66             my @cipos = _get_info($info,'CIPOS');
  67             my @ciend = _get_info($info,'CIEND');
  68             my @svlen = _get_info($info,'SVLEN');
  69
  70             my %data_obj = (
  71                 additionalInfo => {},
  72                 alternate_bases => $_->{alt},
  73                 ciend => [@ciend],
  74                 cipos => [@cipos],
  75                 created => undef,
  76                 end => $_->{pos} + length($_->{ref}),
  77                 filtersApplied => $_->{filter} eq "." ? JSON::false : JSON::true,
  78                 filtersFailed => ( $_->{filter} eq "PASS" || $_->{filter} eq "." ) ? undef : $_->{filter},
  79                 filtersPassed => $_->{filter} eq "PASS" ? JSON::true : JSON::false,
  80                 referenceBases => $_->{ref},
  81                 referenceName =>  $_->{chrom} ? $_->{chrom} : undef,
  82                 start => $_->{pos},
  83                 svlen => @svlen,
  84                 updated => undef,
  85                 variantDbId => qq|$_->{marker_name}|,
  86                 variantNames => $_->{marker_name},
  87                 variantSetDbId => _quote($_->{project_id}, $_->{nd_protocol_id} ),
  88                 variantType => $svtype,
  89             );
  90             push @data_out, \%data_obj;
  91         }
  92         $counter++;
  93     }
  94
  95     my %result = (data=>\@data_out);
  96     my @data_files;
  97     my $pagination = CXGN::BrAPI::Pagination->pagination_response($counter,$page_size,$page);
  98     return CXGN::BrAPI::JSONResponse->return_success(\%result, $pagination, \@data_files, $status, 'Variants result constructed');
  99 }
 100
 101 sub detail {
 102     my $self = shift;
 103     my $inputs = shift;
 104     my $page_size = $self->page_size;
 105     my $page = $self->page;
 106     my $status = $self->status;
 107     my @marker_ids;
 108
 109     my $marker_ids = $inputs->{variantDbId};
 110
 111     my $schema = $self->bcs_schema;
 112     my @data_out;
 113
 114
 115     my $marker_search = CXGN::Marker::SearchBrAPI->new({
 116         bcs_schema => $schema,
 117         protocol_id_list => [],
 118         marker_name_list => [$marker_ids],
 119     });
 120
 121     my ($data, $total_count) = $marker_search->search();
 122
 123     foreach (@$data){
 124         my $info = $_->{info};
 125         my $svtype = $1 if ($_->{info} =~ /SVTYPE=(\w+);/) ;
 126         my @cipos = _get_info($info,'CIPOS');
 127         my @ciend = _get_info($info,'CIEND');
 128         my @svlen = _get_info($info,'SVLEN');
 129
 130         my %data_obj = (
 131             additionalInfo => {},
 132             alternate_bases => $_->{alt},
 133             ciend => [@ciend],
 134             cipos => [@cipos],
 135             created => undef,
 136             end => $_->{pos} + length($_->{ref}),
 137             filtersApplied => $_->{filter} eq "." ? JSON::false : JSON::true,
 138             filtersFailed => ( $_->{filter} eq "PASS" || $_->{filter} eq "." ) ? undef : $_->{filter},
 139             filtersPassed => $_->{filter} eq "PASS" ? JSON::true : JSON::false,
 140             referenceBases => $_->{ref},
 141             referenceName =>  $_->{chrom} ? 'chr_' . $_->{chrom} : undef,
 142             start => $_->{pos},
 143             svlen => @svlen, #length($_->{alt}),
 144             updated => undef,
 145             variantDbId => qq|$_->{marker_name}|,
 146             variantNames => $_->{marker_name},
 147             variantSetDbId => _quote($_->{project_id}, $_->{nd_protocol_id} ),
 148             variantType => $svtype,
 149         );
 150         push @data_out, \%data_obj;
 151     }
 152
 153     my %result = (data=>\@data_out);
 154     my @data_files;
 155     my $pagination = CXGN::BrAPI::Pagination->pagination_response(1,$page_size,$page);
 156     return CXGN::BrAPI::JSONResponse->return_success(\%result, $pagination, \@data_files, $status, 'Variants result constructed');
 157 }
 158
 159
 160 sub calls {
 161     my $self = shift;
 162     my $inputs = shift;
 163     my $c = $self->context;
 164     my $page_size = $self->page_size;
 165     my $page = $self->page;
 166     my $status = $self->status;
 167     my $sep_phased = $inputs->{sep_phased};
 168     my $sep_unphased = $inputs->{sep_unphased};
 169     my $unknown_string = $inputs->{unknown_string};
 170     my $expand_homozygotes = $inputs->{expand_homozygotes};
 171     my $marker_id = $inputs->{variantDbId};
 172     my @trial_ids;
 173
 174     if ($sep_phased || $sep_unphased || $expand_homozygotes || $unknown_string){
 175         push @$status, { 'error' => 'The following parameters are not implemented: expandHomozygotes, unknownString, sepPhased, sepUnphased' };
 176     }
 177
 178     my $trial_search = CXGN::Trial::Search->new({
 179         bcs_schema=>$self->bcs_schema,
 180         trial_design_list=>['genotype_data_project']
 181     });
 182     my ($data, $total_count) = $trial_search->search();
 183
 184     foreach (@$data){
 185         push @trial_ids, $_->{trial_id};
 186     }
 187
 188     my @data_files;
 189     my %result;
 190
 191     my $genotypes_search = CXGN::Genotype::Search->new({
 192         bcs_schema=>$self->bcs_schema,
 193         cache_root=>$c->config->{cache_file_path},
 194         people_schema => $self->people_schema(),
 195         trial_list=>\@trial_ids,
 196         genotypeprop_hash_select=>['DS', 'GT', 'NT'],
 197         protocolprop_top_key_select=>[],
 198         protocolprop_marker_hash_select=>[],
 199     });
 200     my $file_handle = $genotypes_search->get_cached_file_search_json($c->config->{cluster_shared_tempdir}, 0);
 201
 202     my $start_index = $page*$page_size;
 203     my $end_index = $page*$page_size + $page_size - 1;
 204     my $counter = 0;
 205
 206     open my $fh, "<&", $file_handle or die "Can't open output file: $!";
 207     my $header_line = <$fh>;
 208
 209     my @data;
 210
 211     while (my $gt_line = <$fh>) {
 212         my $gt = decode_json $gt_line;
 213         my $genotype = $gt->{selected_genotype_hash};
 214         my @ordered_refmarkers = sort keys(%$genotype);
 215         my $genotypeprop_id = $gt->{markerProfileDbId};
 216
 217         foreach my $m (@ordered_refmarkers) {
 218             if ($m eq $marker_id){
 219                 if ($counter >= $start_index && $counter <= $end_index) {
 220                     my $geno = '';
 221                     if (exists($genotype->{$m}->{'NT'}) && defined($genotype->{$m}->{'NT'})){
 222                         $geno = $genotype->{$m}->{'NT'};
 223                     }
 224                     elsif (exists($genotype->{$m}->{'GT'}) && defined($genotype->{$m}->{'GT'})){
 225                         $geno = $genotype->{$m}->{'GT'};
 226                     }
 227                     elsif (exists($genotype->{$m}->{'DS'}) && defined($genotype->{$m}->{'DS'})){
 228                         $geno = $genotype->{$m}->{'DS'};
 229                     }
 230                     push @data, {
 231                         additionalInfo=>undef,
 232                         variantName=>qq|$m|,
 233                         variantDbId=>qq|$m|,
 234                         callSetDbId=>qq|$gt->{stock_id}|,
 235                         callSetName=>qq|$gt->{stock_name}|,
 236                         genotype=>{values=>$geno},
 237                         genotype_likelihood=>undef,
 238                         phaseSet=>undef,
 239                     };
 240                 }
 241                 $counter++;
 242             }
 243         }
 244     }
 245
 246     %result = ( data=>\@data,
 247                 expandHomozygotes=>undef,
 248                 sepPhased=>undef,
 249                 sepUnphased=>undef,
 250                 unknownString=>undef);
 251
 252
 253
 254     my $pagination = CXGN::BrAPI::Pagination->pagination_response($counter,$page_size,$page);
 255     return CXGN::BrAPI::JSONResponse->return_success(\%result, $pagination, \@data_files, $status, 'VariantSets result constructed');
 256 }
 257
 258 sub _get_info {
 259     my $info = shift;
 260     my $item = shift;
 261     my @array = [];
 262
 263     #match with CIPOS=-22,18;CIEND=-12,32"
 264     if ( $info =~ /$item=(-?(\d+),?)+/) {
 265         my $match = $&;
 266         $match =~ s/$item=//g;
 267         my @splited = split(/,/, $match);
 268         @array = map { $_ + 0 } @splited;
 269     }
 270
 271     return @array ;
 272 }
 273
 274 sub _quote {
 275     my $array = shift;
 276     my $protocol = shift;
 277
 278     foreach (@$array) {
 279         $_ = "$_" . "p". $protocol;
 280     }
 281
 282     return $array
 283 }
 284
 285 1;