lib/SGN/Controller/AJAX/Solgwas.pm

   1 use strict;
   2 use warnings;
   3
   4 package SGN::Controller::AJAX::Solgwas;
   5
   6 use Moose;
   7 use Data::Dumper;
   8 use File::Temp qw | tempfile |;
   9 use File::Slurp;
  10 use File::Spec qw | catfile|;
  11 use File::Basename qw | basename |;
  12 use File::Copy;
  13 use CXGN::Dataset;
  14 use CXGN::Dataset::File;
  15 #use SGN::Model::Cvterm;
  16 #use CXGN::List;
  17 #use CXGN::List::Validate;
  18 #use CXGN::Trial::Download;
  19 #use CXGN::Phenotypes::PhenotypeMatrix;
  20 #use CXGN::BreederSearch;
  21 use CXGN::Tools::Run;
  22 use Cwd qw(cwd);
  23
  24 BEGIN { extends 'Catalyst::Controller::REST' }
  25
  26 __PACKAGE__->config(
  27     default   => 'application/json',
  28     stash_key => 'rest',
  29     map       => { 'application/json' => 'JSON' },
  30     );
  31
  32
  33 sub shared_phenotypes: Path('/ajax/solgwas/shared_phenotypes') : {
  34     my $self = shift;
  35     my $c = shift;
  36     my $dataset_id = $c->req->param('dataset_id');
  37     my $exclude_outliers = $c->req->param('dataset_trait_outliers');
  38
  39     my $people_schema = $c->dbic_schema("CXGN::People::Schema");
  40     my $schema = $c->dbic_schema("Bio::Chado::Schema", "sgn_chado");
  41     my $ds = CXGN::Dataset->new(people_schema => $people_schema, schema => $schema, sp_dataset_id => $dataset_id);
  42     my $traits = $ds->retrieve_traits();
  43     my @trait_info;
  44     foreach my $t (@$traits) {
  45               my $tobj = CXGN::Cvterm->new({ schema=>$schema, cvterm_id => $t->[0] });
  46         push @trait_info, [ $tobj->cvterm_id(), $tobj->name()];
  47     }
  48
  49     # my $solgwas_tmp_output = $c->config->{cluster_shared_tempdir}."/solgwas_files";
  50     # mkdir $solgwas_tmp_output if ! -d $solgwas_tmp_output;
  51     # my ($fh, $tempfile) = tempfile(
  52     # "trait_XXXXXX",
  53     #   DIR=> $solgwas_tmp_output,
  54     # );
  55
  56     $c->tempfiles_subdir("solgwas_files");
  57     my ($fh, $tempfile) = $c->tempfile(TEMPLATE=>"solgwas_files/trait_XXXXX");
  58     #my $tmp_dir = File::Spec->catfile($c->config->{basepath}, 'gwas_tmpdir');
  59 #    my $solgwas_tmp_output = $c->config->{cluster_shared_tempdir}."/solgwas_files";
  60 #    mkdir $solgwas_tmp_output if ! -d $solgwas_tmp_output;
  61 #    my ($tmp_fh, $tempfile) = tempfile(
  62 #      "solgwas_download_XXXXX",
  63 #      DIR=> $solgwas_tmp_output,
  64 #    );
  65 #    my $pheno_filepath = $tempfile . "_phenotype.txt";
  66
  67     my $temppath = $c->config->{basepath}."/".$tempfile;
  68 #    my $temppath = $solgwas_tmp_output . "/" . $tempfile;
  69     my $ds2 = CXGN::Dataset::File->new(people_schema => $people_schema, schema => $schema, sp_dataset_id => $dataset_id, exclude_dataset_outliers => $exclude_outliers, file_name => $temppath, quotes => 0);
  70     my $phenotype_data_ref = $ds2->retrieve_phenotypes();
  71
  72 #    my $phenotypes = $ds->retrieve_phenotypes();
  73 #    my $trials_ref = $ds->retrieve_trials();
  74     print STDERR Dumper(@trait_info);
  75 #    my @trials = @$trials_ref;
  76
  77 #    my $values_path = $c->{basepath} . "./documents/tempfiles/solgwas_files/";
  78 #    copy($pheno_filepath,$values_path);
  79
  80 #    my $file_basename = basename($pheno_filepath);
  81 #    my $file_response = "./documents/tempfiles/solgwas_files/" . $file_basename;
  82 #    print STDERR $file_response . "\n";
  83 #    my @co_pheno;
  84     $c->stash->{rest} = {
  85         options => \@trait_info,
  86         tempfile => $tempfile."_phenotype.txt",
  87 #        tempfile => $file_response,
  88     };
  89 }
  90
  91
  92 sub extract_trait_data :Path('/ajax/solgwas/getdata') Args(0) {
  93     my $self = shift;
  94     my $c = shift;
  95
  96     my $file = $c->req->param("file");
  97     my $trait = $c->req->param("trait");
  98
  99     $file = basename($file);
 100
 101     my $temppath = File::Spec->catfile($c->config->{basepath}, "static/documents/tempfiles/solgwas_files/".$file);
 102 #    my $temppath = File::Spec->catfile($c->config->{cluster_shared_tempdir}, "static/documents/tempfiles/solgwas_files/".$file);
 103 #    my $temppath = File::Spec->catfile($c->config->{basepath}, "static/documents/tempfiles/solgwas_files/solgwas_download_0bDQ5_phenotype.txt");
 104     print STDERR Dumper($temppath);
 105
 106     my $F;
 107     if (! open($F, "<", $temppath)) {
 108         $c->stash->{rest} = { error => "Can't find data." };
 109         return;
 110     }
 111
 112     my $header = <$F>;
 113     chomp($header);
 114     print STDERR Dumper($header);
 115     my @keys = split("\t", $header);
 116     print STDERR Dumper($keys[1]);
 117 # add this for loop to remove the crop ontology codes from the keys (and the preceding pipes)
 118     for(my $n=0; $n <@keys; $n++) {
 119         if ($keys[$n] =~ /\|CO\_/) {
 120         $keys[$n] =~ s/\|CO\_.*//;
 121         }
 122     }
 123     my @data = ();
 124
 125     while (<$F>) {
 126         chomp;
 127
 128         my @fields = split "\t";
 129         my %line = ();
 130         for(my $n=0; $n <@keys; $n++) {
 131             if (exists($fields[$n]) && defined($fields[$n])) {
 132                 $line{$keys[$n]}=$fields[$n];
 133             }
 134         }
 135     print STDERR Dumper(\%line);
 136         push @data, \%line;
 137     }
 138
 139     $c->stash->{rest} = { data => \@data, trait => $trait};
 140 }
 141
 142 sub generate_pca: Path('/ajax/solgwas/generate_pca') : {
 143     my $self = shift;
 144     my $c = shift;
 145     my $dataset_id = $c->req->param('dataset_id');
 146     my $trait_id = $c->req->param('trait_id');
 147     my $pc_check = $c->req->param('pc_check');
 148     my $kinship_check = $c->req->param('kinship_check');
 149         my $forbid_cache = defined($c->req->param('forbid_cache')) ? $c->req->param('forbid_cache') : 0;
 150
 151
 152     print STDERR $dataset_id;
 153     print STDERR $trait_id;
 154     $c->tempfiles_subdir("solgwas_files");
 155 #    my ($fh, $tempfiletest) = $c->tempfile(TEMPLATE=>"solgwas_files/solgwas_download_XXXXX");
 156     my $solgwas_tmp_output = $c->config->{cluster_shared_tempdir}."/solgwas_files";
 157     mkdir $solgwas_tmp_output if ! -d $solgwas_tmp_output;
 158     my ($tmp_fh, $tempfile) = tempfile(
 159       "solgwas_download_XXXXX",
 160       DIR=> $solgwas_tmp_output,
 161     );
 162     #my $tmp_dir = File::Spec->catfile($c->config->{basepath}, 'gwas_tmpdir');
 163     my $pheno_filepath = $tempfile . "_phenotype.txt";
 164     my $geno_filepath = $tempfile . "_genotype.txt";
 165 #    my $pheno_filepath = "." . $tempfile . "_phenotype.txt";
 166 #    my $geno_filepath = "." . $tempfile . "_genotype.txt";
 167     my $people_schema = $c->dbic_schema("CXGN::People::Schema");
 168     my $schema = $c->dbic_schema("Bio::Chado::Schema", "sgn_chado");
 169 #    my $temppath = $c->config->{basepath}."/".$tempfile;
 170 #    my $temppath = $c->config->{cluster_shared_tempdir}."/".$tempfile;
 171 #    my $temppath = $solgwas_tmp_output . "/" . $tempfile;
 172     my $temppath = "/" . $tempfile;
 173
 174 #    my $ds = CXGN::Dataset::File->new(people_schema => $people_schema, schema => $schema, sp_dataset_id => $dataset_id, file_name => $temppath);
 175     my $ds = CXGN::Dataset::File->new(people_schema => $people_schema, schema => $schema, sp_dataset_id => $dataset_id, file_name => $temppath, quotes => 0);
 176
 177     ##    my $phenotype_data_ref = $ds->retrieve_phenotypes();
 178     my $phenotype_data_ref = $ds->retrieve_phenotypes($pheno_filepath);
 179     my $protocols = $ds->retrieve_genotyping_protocols();
 180     my $protocol_id;
 181     foreach (@$protocols) {
 182         $protocol_id = $_->[0];
 183     }
 184
 185 #    my ($fh, $tempfile2) = $c->tempfile(TEMPLATE=>"solgwas_files/solgwas_genotypes_download_XXXXX");
 186 #    my $temppath2 = $c->config->{basepath}."/".$tempfile2;
 187 #    my $ds2 = CXGN::Dataset::File->new(people_schema => $people_schema, schema => $schema, sp_dataset_id => $dataset_id, file_name => $temppath2);
 188     #    $ds2 -> file_name => $temppath2;
 189
 190     my $filehandle = $ds->retrieve_genotypes($protocol_id,$geno_filepath, $c->config->{cache_file_path}, $c->config->{cluster_shared_tempdir}, $c->config->{backend}, $c->config->{cluster_host}, $c->config->{'web_cluster_queue'}, $c->config->{basepath}, $forbid_cache);
 191 #    my $base_filename = $$filehandle;
 192     print STDERR $filehandle . "\n";
 193 #    print STDERR $base_filename . "\n";
 194 #    $ds-> @$trials_ref = retrieve_genotypes();
 195     my $newtrait = $trait_id;
 196     $newtrait =~ s/\s/\_/g;
 197     $newtrait =~ s/\//\_/g;
 198     print STDERR $newtrait . "\n";
 199 #    my $figure1file = "." . $tempfile . "_" . $newtrait . "_figure1.png";
 200 #    my $figure2file = "." . $tempfile . "_" . $newtrait . "_figure2.png";
 201 #    my $figure3file = "." . $tempfile . "_" . $newtrait . "_figure3.png";
 202 #    my $figure4file = "." . $tempfile . "_" . $newtrait . "_figure4.png";
 203     my $tempfile2 = $tempfile;
 204     my $figure1file = $tempfile . "_" . $newtrait . "_figure1.png";
 205     my $figure2file = $tempfile . "_" . $newtrait . "_figure2.png";
 206     my $figure3file = $tempfile . "_" . $newtrait . "_figure3.png";
 207     my $figure4file = $tempfile . "_" . $newtrait . "_figure4.png";
 208
 209     $trait_id =~ tr/ /./;
 210     $trait_id =~ tr/\//./;
 211 #    my $clean_cmd = "rm /home/vagrant/cxgn/sgn/documents/tempfiles/solgwas_files/SolGWAS_Figure*.png";
 212 #    system($clean_cmd);
 213     my $geno_filepath2 = $tempfile . "_genotype.txt";
 214 #    my $geno_filepath2 = $base_filename . "_genotype_edit.txt";
 215 #    my $edit_cmd = "sed -e '1 s/\^/row.names\t/' " . $base_filename . " > " . $geno_filepath2;
 216 #    system($edit_cmd);
 217 #    my $geno_filepath3 = "." . $tempfile . "_genotype_edit_subset.txt";
 218     my $geno_filepath3 = $tempfile . "_genotype_edit_subset.txt";
 219
 220 #    my $trim_cmd = "cut -f 1-50 " . $geno_filepath2 . " > " . $geno_filepath3;
 221 #    system($trim_cmd);
 222
 223 #    open my $filehandle_in2,  "<", "$geno_filepath2"  or die "Could not open $geno_filepath2: $!\n";
 224     open my $filehandle_out, ">", "$geno_filepath2" or die "Could not create $geno_filepath2: $!\n";
 225
 226     my $marker_total;
 227
 228     while ( my $line = <$filehandle> ) {
 229         my @sample_line = (split /\s+/, $line);
 230         $marker_total = scalar(@sample_line);
 231         print $filehandle_out $line;
 232     }
 233     close $filehandle;
 234     close $filehandle_out;
 235
 236 #
 237 # # Hardcoded number of markers to be selected - make this selectable by user?
 238 #     my $markers_selected = 500;
 239 # #    my @column_selection = (0,2);
 240 # # Initialize column selection so the row.names are selected first
 241 #     my @column_selection = (0);
 242 #     my %columns_seen;
 243 #     for (my $i=0; $i <= $markers_selected; $i++) {
 244 #         my $random_current = int(rand($marker_total));
 245 #         redo if $columns_seen{$random_current}++;
 246 #         push @column_selection, $random_current;
 247 #         print STDERR $random_current . "\n";
 248 #     }
 249 #
 250 #     open my $filehandle_in, "<", "$geno_filepath2"  or die "Could not open $geno_filepath2: $!\n";
 251 #     open my $filehandle_out2, ">", "$geno_filepath3" or die "Could not create $geno_filepath3: $!\n";
 252 #
 253 # #    foreach my $item (@column_selection) {
 254 #     while ( my $line = <$filehandle_in> ) {
 255 #         my $curr_line;
 256 #         my @first_item = (split /\s+/, $line);
 257 #         foreach my $item (@column_selection) {
 258 #             $curr_line .= $first_item[$item] . "\t";
 259 #         }
 260 # #           $curr_line .= "\n";
 261 #         print STDERR $curr_line . "\n";
 262 #         print $filehandle_out2 "$curr_line\n";
 263 #     }
 264 #
 265 #     close $filehandle_in;
 266 #     close $filehandle_out2;
 267
 268 #    my $cmd = "Rscript " . $c->config->{basepath} . "/R/solgwas/solgwas_script.R " . $pheno_filepath . " " . $geno_filepath3 . " " . $trait_id . " " . $figure3file . " " . $figure4file . " " . $pc_check . " " . $kinship_check;
 269 #    system($cmd);
 270
 271     my $cmd = CXGN::Tools::Run->new(
 272         {
 273             backend => $c->config->{backend},
 274             submit_host => $c->config->{cluster_host},
 275             temp_base => $c->config->{cluster_shared_tempdir} . "/solgwas_files",
 276             queue => $c->config->{'web_cluster_queue'},
 277             do_cleanup => 0,
 278             # don't block and wait if the cluster looks full
 279             max_cluster_jobs => 1_000_000_000,
 280         }
 281     );
 282     $cmd->run_cluster(
 283             "Rscript ",
 284             $c->config->{basepath} . "/R/solgwas/solgwas_genoPCA_script.R",
 285             $geno_filepath2,
 286             $figure2file,
 287     );
 288     $cmd->is_cluster(1);
 289     $cmd->wait;
 290
 291
 292     my $figure_path = "./documents/tempfiles/solgwas_files/";
 293     copy($figure2file,$figure_path);
 294
 295     my $figure2basename = basename($figure2file);
 296     my $figure2file_response = "/documents/tempfiles/solgwas_files/" . $figure2basename;
 297
 298     $c->stash->{rest} = {
 299         figure2 => $figure2file_response,
 300         dummy_response => $dataset_id,
 301         dummy_response2 => $trait_id,
 302     };
 303 }
 304
 305
 306 sub generate_results: Path('/ajax/solgwas/generate_results') : {
 307     my $self = shift;
 308     my $c = shift;
 309     my $dataset_id = $c->req->param('dataset_id');
 310     my $trait_id = $c->req->param('trait_id');
 311     my $pc_check = $c->req->param('pc_check');
 312     my $kinship_check = $c->req->param('kinship_check');
 313         my $forbid_cache = defined($c->req->param('forbid_cache')) ? $c->req->param('forbid_cache') : 0;
 314     my $exclude_outliers = $c->req->param('dataset_trait_outliers');
 315
 316     print STDERR $dataset_id;
 317     print STDERR $trait_id;
 318     $c->tempfiles_subdir("solgwas_files");
 319 #    my ($fh, $tempfiletest) = $c->tempfile(TEMPLATE=>"solgwas_files/solgwas_download_XXXXX");
 320     my $solgwas_tmp_output = $c->config->{cluster_shared_tempdir}."/solgwas_files";
 321     mkdir $solgwas_tmp_output if ! -d $solgwas_tmp_output;
 322     my ($tmp_fh, $tempfile) = tempfile(
 323       "solgwas_download_XXXXX",
 324       DIR=> $solgwas_tmp_output,
 325     );
 326     #my $tmp_dir = File::Spec->catfile($c->config->{basepath}, 'gwas_tmpdir');
 327     my $pheno_filepath = $tempfile . "_phenotype.txt";
 328     my $geno_filepath = $tempfile . "_genotype.txt";
 329 #    my $pheno_filepath = "." . $tempfile . "_phenotype.txt";
 330 #    my $geno_filepath = "." . $tempfile . "_genotype.txt";
 331     my $people_schema = $c->dbic_schema("CXGN::People::Schema");
 332     my $schema = $c->dbic_schema("Bio::Chado::Schema", "sgn_chado");
 333 #    my $temppath = $c->config->{basepath}."/".$tempfile;
 334 ##    my $temppath = $c->config->{cluster_shared_tempdir}."/".$tempfile;
 335     #    my $temppath = $solgwas_tmp_output . "/" . $tempfile;
 336     my $temppath = $tempfile;
 337
 338 #    my $ds = CXGN::Dataset::File->new(people_schema => $people_schema, schema => $schema, sp_dataset_id => $dataset_id, file_name => $temppath);
 339
 340     my $ds = CXGN::Dataset::File->new(people_schema => $people_schema, schema => $schema, sp_dataset_id => $dataset_id, exclude_dataset_outliers => $exclude_outliers, file_name => $temppath, quotes => 0);
 341
 342 ##    my $phenotype_data_ref = $ds->retrieve_phenotypes();
 343     my $phenotype_data_ref = $ds->retrieve_phenotypes($pheno_filepath);
 344     my $protocols = $ds->retrieve_genotyping_protocols();
 345     my $protocol_id;
 346     foreach (@$protocols) {
 347         $protocol_id = $_->[0];
 348     }
 349
 350 #    my ($fh, $tempfile2) = $c->tempfile(TEMPLATE=>"solgwas_files/solgwas_genotypes_download_XXXXX");
 351 #    my $temppath2 = $c->config->{basepath}."/".$tempfile2;
 352 #    my $ds2 = CXGN::Dataset::File->new(people_schema => $people_schema, schema => $schema, sp_dataset_id => $dataset_id, file_name => $temppath2);
 353     #    $ds2 -> file_name => $temppath2;
 354
 355     my %chromList;
 356     my %posList;
 357     my $name;
 358     my @row;
 359     my $chrom;
 360     my $pos;
 361     my $q = "SELECT s.value->>'name', s.value->>'chrom', s.value->>'pos' from nd_protocolprop, jsonb_each(nd_protocolprop.value) s(key, value) where type_id = (SELECT cvterm_id FROM public.cvterm WHERE name = 'vcf_map_details_markers') and nd_protocol_id = $protocol_id";
 362     my $sth = $c->dbc->dbh->prepare($q);
 363     $sth->execute();
 364     while (@row = $sth->fetchrow_array) {
 365         $name = $row[0];
 366         $chromList{$name} = $row[1];
 367         $posList{$name} = $row[2];
 368     }
 369
 370     my $filehandle = $ds->retrieve_genotypes($protocol_id,$geno_filepath, $c->config->{cache_file_path}, $c->config->{cluster_shared_tempdir}, $c->config->{backend}, $c->config->{cluster_host}, $c->config->{'web_cluster_queue'}, $c->config->{basepath}, $forbid_cache);
 371 #    my $base_filename = $$filehandle;
 372     print STDERR $filehandle . "\n";
 373 #    print STDERR $base_filename . "\n";
 374 #    $ds-> @$trials_ref = retrieve_genotypes();
 375     my $newtrait = $trait_id;
 376     $newtrait =~ s/\s/\_/g;
 377     $newtrait =~ s/\//\_/g;
 378     $newtrait =~ s/[|%()]/\./g;
 379     print STDERR $newtrait . "\n";
 380 #    my $figure1file = "." . $tempfile . "_" . $newtrait . "_figure1.png";
 381 #    my $figure2file = "." . $tempfile . "_" . $newtrait . "_figure2.png";
 382 #    my $figure3file = "." . $tempfile . "_" . $newtrait . "_figure3.png";
 383 #    my $figure4file = "." . $tempfile . "_" . $newtrait . "_figure4.png";
 384     my $tempfile2 = $tempfile;
 385     my $figure1file = $tempfile . "_" . $newtrait . "_figure1.png";
 386     my $figure2file = $tempfile . "_" . $newtrait . "_figure2.png";
 387     my $figure3file = $tempfile . "_" . $newtrait . "_figure3.png";
 388     my $figure4file = $tempfile . "_" . $newtrait . "_figure4.png";
 389     my $gwasResultsPhenoCsv = $tempfile . "_" . $newtrait . "_gwasresults_pheno.csv";
 390
 391     $trait_id =~ tr/ /./;
 392     $trait_id =~ tr/\//./;
 393 #    my $clean_cmd = "rm /home/vagrant/cxgn/sgn/documents/tempfiles/solgwas_files/SolGWAS_Figure*.png";
 394 #    system($clean_cmd);
 395     my $geno_filepath2 = $tempfile . "_genotype.txt";
 396 #    my $geno_filepath2 = $base_filename . "_genotype_edit.txt";
 397 #    my $edit_cmd = "sed -e '1 s/\^/row.names\t/' " . $base_filename . " > " . $geno_filepath2;
 398 #    system($edit_cmd);
 399 #    my $geno_filepath3 = "." . $tempfile . "_genotype_edit_subset.txt";
 400     my $geno_filepath3 = $tempfile . "_genotype_edit_subset.txt";
 401
 402 #    my $trim_cmd = "cut -f 1-50 " . $geno_filepath2 . " > " . $geno_filepath3;
 403 #    system($trim_cmd);
 404
 405     open my $filehandle_out, ">", "$geno_filepath2" or die "Could not create $geno_filepath2: $!\n";
 406     my $line = <$filehandle>;
 407     my @sample_line = (split /\t/, $line);
 408     splice(@sample_line, 1, 0, "chrom");
 409     splice(@sample_line, 2, 0, "pos");
 410     $line = join("\t", @sample_line);
 411     print $filehandle_out $line;
 412     my $marker_total;
 413
 414     while ( my $line = <$filehandle> ) {
 415         @sample_line = split(/\t/, $line);
 416         if ($chromList{$sample_line[0]}) {
 417             $chrom = $chromList{$sample_line[0]};
 418         } elsif ($sample_line[0] =~ /\_/) {
 419             ($chrom, undef) = split /\_/, $sample_line[0];
 420             print STDERR "Warning! no chrom data, using $chrom extracted from $sample_line[0]\n";
 421         } else {
 422             $chrom = "";
 423         }
 424         if ($posList{$sample_line[0]}) {
 425             $pos = $posList{$sample_line[0]};
 426         } elsif ($sample_line[0] =~ /\_/) {
 427             (undef, $pos) = split /\_/, $sample_line[0];
 428             print STDERR "Warning! No position data, using $pos extracted from $sample_line[0]\n";
 429         } else {
 430             $pos = "";
 431         }
 432         splice(@sample_line, 1, 0, $chrom);
 433         splice(@sample_line, 2, 0, $pos);
 434         $line = join("\t", @sample_line);
 435         print $filehandle_out $line;
 436     }
 437     close $filehandle;
 438     close $filehandle_out;
 439
 440 #
 441 # # Hardcoded number of markers to be selected - make this selectable by user?
 442 #     my $markers_selected = 500;
 443 # #    my @column_selection = (0,2);
 444 # # Initialize column selection so the row.names are selected first
 445 #     my @column_selection = (0);
 446 #     my %columns_seen;
 447 #     for (my $i=0; $i <= $markers_selected; $i++) {
 448 #         my $random_current = int(rand($marker_total));
 449 #         redo if $columns_seen{$random_current}++;
 450 #         push @column_selection, $random_current;
 451 #         print STDERR $random_current . "\n";
 452 #     }
 453 #
 454 #     open my $filehandle_in, "<", "$geno_filepath2"  or die "Could not open $geno_filepath2: $!\n";
 455 #     open my $filehandle_out2, ">", "$geno_filepath3" or die "Could not create $geno_filepath3: $!\n";
 456 #
 457 # #    foreach my $item (@column_selection) {
 458 #     while ( my $line = <$filehandle_in> ) {
 459 #         my $curr_line;
 460 #         my @first_item = (split /\s+/, $line);
 461 #         foreach my $item (@column_selection) {
 462 #             $curr_line .= $first_item[$item] . "\t";
 463 #         }
 464 # #           $curr_line .= "\n";
 465 #         print STDERR $curr_line . "\n";
 466 #         print $filehandle_out2 "$curr_line\n";
 467 #     }
 468 #
 469 #     close $filehandle_in;
 470 #     close $filehandle_out2;
 471
 472 #    my $cmd = "Rscript " . $c->config->{basepath} . "/R/solgwas/solgwas_script.R " . $pheno_filepath . " " . $geno_filepath3 . " " . $trait_id . " " . $figure3file . " " . $figure4file . " " . $pc_check . " " . $kinship_check;
 473 #    system($cmd);
 474     my $cmd = CXGN::Tools::Run->new(
 475         {
 476             backend => $c->config->{backend},
 477             submit_host => $c->config->{cluster_host},
 478             temp_base => $c->config->{cluster_shared_tempdir} . "/solgwas_files",
 479             queue => $c->config->{'web_cluster_queue'},
 480             do_cleanup => 0,
 481             # don't block and wait if the cluster looks full
 482             max_cluster_jobs => 1_000_000_000,
 483         }
 484     );
 485     $cmd->run_cluster(
 486             "Rscript ",
 487             $c->config->{basepath} . "/R/solgwas/solgwas_script.R",
 488             $pheno_filepath,
 489             $geno_filepath2,
 490             $trait_id,
 491             $figure3file,
 492             $figure4file,
 493             $pc_check,
 494             $kinship_check,
 495             $gwasResultsPhenoCsv,
 496     );
 497
 498     $cmd->is_cluster(1);
 499     $cmd->wait;
 500
 501     my $figure_path = "./documents/tempfiles/solgwas_files/";
 502     copy($figure3file,$figure_path);
 503     copy($figure4file,$figure_path);
 504     copy($gwasResultsPhenoCsv,$figure_path);
 505 #    my $figure3basename = $figure3file;
 506
 507 #    $figure3basename =~ s/\/export\/prod\/tmp\/solgwas\_files\///;
 508     my $figure3basename = basename($figure3file);
 509     my $figure3file_response = "/documents/tempfiles/solgwas_files/" . $figure3basename;
 510     my $figure4basename = basename($figure4file);
 511     my $figure4file_response = "/documents/tempfiles/solgwas_files/" . $figure4basename;
 512     my $gwasResultsCsvBasename = basename($gwasResultsPhenoCsv);
 513     my $gwasCsv_response = "/documents/tempfiles/solgwas_files/" . $gwasResultsCsvBasename;
 514 #    $figure4file_response =~ s/\.\/static//;
 515     $c->stash->{rest} = {
 516         figure3         => $figure3file_response,
 517         figure4         => $figure4file_response,
 518         dummy_response  => $dataset_id,
 519         dummy_response2 => $trait_id,
 520         gwas_csv_response  => $gwasCsv_response,
 521     };
 522 }
 523
 524 1;