lib/SGN/Controller/motifs_finder.pm

   1 package SGN::Controller::motifs_finder;
   2
   3 use Moose;
   4 use namespace::autoclean;
   5 use File::Temp qw | tempfile |;
   6 use File::Basename;
   7 use Data::Dumper;
   8
   9
  10 BEGIN { extends 'Catalyst::Controller'; }
  11
  12 =head1 NAME
  13
  14 motifs_finder::Controller::motifs_finder - Catalyst Controller
  15
  16 =head1 DESCRIPTION
  17
  18 Catalyst Controller.
  19
  20 =head1 METHODS
  21
  22 =cut
  23
  24 =head2 index
  25
  26 =cut
  27
  28 sub index :Path('/tools/motifs_finder/') :Args(0) {
  29    my ( $self, $c ) = @_;
  30
  31    $c->stash->{template} = '/tools/motifs_finder/index.mas';
  32 }
  33
  34 sub name_var :Path('/test/') :Args(0) {
  35     my ($self, $c) = @_;
  36
  37      # get variables from catalyst object
  38     my $params = $c->req->body_params();
  39     my $sequence = $c->req->param("sequence");
  40     my $widths_of_motifs = $c->req->param("widths_of_motifs");
  41     my $numbers_of_sites = $c->req->param("numbers_of_sites");
  42     my $seq_file = $c->req->param("sequence_file");
  43     my $no_of_seeds = $c->req->param("number_of_seeds");
  44     my $fragmentation = $c->req->param("fragmentation");
  45     my $rev_complement = $c->req->param("rev_complement");
  46     my $weblogo_output = $c->config->{tmp_weblogo_path};
  47     my $basePath = $c->config->{tempfiles_base_motifs_finder};
  48     my $cluster_shared_bindir = $c->config->{cluster_motifs_finder};
  49
  50   # validate the Nucleic Acid in sequence. To ensure the return of line is not seen as a space.
  51         my @seq;
  52         my @errors;
  53
  54     # to generate temporary file name for the analysis
  55     my ($fh, $filename) =tempfile("XXXXX", DIR => "$basePath/static/documents/tempfiles/motifs_finder/");
  56     #my ($fh, $filename) =tempfile("XXXXX", DIR => "$basePath/motifs_finder/");
  57
  58     print STDERR Dumper($filename);
  59         if ($sequence !~ /^>/ && $seq_file eq '')  {
  60                 push ( @errors , "Please, paste sequences or attach sequence file.<br/>Ensure your sequence conform with 'usage help' description.\n");
  61         }
  62
  63         # To send error file to index.mas
  64         if (scalar (@errors) > 0){
  65                 my $user_errors = join("<br />", @errors);
  66                 $c->stash->{error_msg} = join("<br/>", @errors);
  67                 $c->stash->{template} = '/tools/motifs_finder/index.mas';
  68                 return;
  69         }
  70         else {
  71            # If no error prepare the sequence file for sampling
  72            if ($sequence =~ /^>/) {
  73                         $sequence =~ s/[ \,\-\.\#\(\)\%\'\"\[\]\{\}\:\;\=\+\\\/]/_/gi;
  74                         @seq = split(/\s/,$sequence);
  75
  76                 #to open and write and print the input file
  77                 open (my $out_fh, ">", $filename."_input.txt") || die ("\nERROR: the file ".$filename."_input.txt could not be found\n");
  78                 print $out_fh join("\n",@seq);
  79
  80                 # to run Gibbs motifs sampler
  81                 my $err = system("$cluster_shared_bindir/Gibbs.linux ".$filename."_input.txt $widths_of_motifs $numbers_of_sites -W 0.8 -w 0.1 -p 50 -j 5 -i 500 $fragmentation $rev_complement -Z -S $no_of_seeds -C 0.5 -y -nopt -o ".$filename."_output -n");
  82                 print STDOUT "print $err\n";
  83             }
  84             elsif ($seq_file) {
  85                 my $err = system("$cluster_shared_bindir/Gibbs.linux $seq_file $widths_of_motifs $numbers_of_sites -W 0.8 -w 0.1 -p 50 -j 5 -i 500 $fragmentation $rev_complement -Z -S $no_of_seeds -C 0.5 -y -nopt -o ".$filename."_output -n");
  86                 print STDOUT "print $err\n";
  87             }
  88
  89             open (my $output_fh, "<", $filename."_output") || die ("\nERROR: the file ".$filename."_output could not be found\n"); # open sampler output file and write into a FH
  90
  91             # Creating motifs fasta file for weblogo use and other files that are made into tables in the output.mas
  92
  93                 my $switch = 0;
  94                 my $motif = 0;
  95                 my $switch_logo = 0;
  96                 my $logo = 0;
  97                 my @string_result;
  98                 my $logo_file;
  99                 my $wl_out_fh;
 100                 my @motif_element;
 101                 my @logo_image;
 102                 my @logofile_id;
 103                 my $lf_id;
 104                 my @motif_width;
 105                 my @aa;
 106                 my @motif_table_file;
 107                 my $motif_tab_fh;
 108                 my $motif_tab;
 109                 my $freq_tab_switch = 0;
 110                 my $freq_tab_fh;
 111                 my $freq_tab = 0;
 112                 my $freq_tab_file;
 113                 my @freq_tab;
 114                 my $prob_tab_switch = 0;
 115                 my $prob_tab_fh;
 116                 my $prob_tab = 0;
 117                 my $prob_tab_file;
 118                 my @prob_tab;
 119                 my $BGPM_tab_switch = 0;
 120                 my $BGPM_tab_fh;
 121                 my $BGPM_tab = 0;
 122                 my $BGPM_tab_file;
 123                 my @BGPM_tab;
 124                 my $sum_indv_tab_switch = 0;
 125                 my $sum_indv_tab_fh;
 126                 my $sum_indv_tab = 0;
 127                 my $sum_indv_tab_file;
 128                 my @sum_indv_tab;
 129                 my $sum = 0;
 130                 my $switch_sum = 0;
 131                 my @sum;
 132
 133             while (my $line = <$output_fh>) {
 134                 chomp $line;
 135                 push @string_result, $line;
 136                 if ($line =~ m/^Log\sBackground\sportion\sof\sMap\s\=\s/){
 137                                 $sum = 1;
 138                 }
 139                 if ($sum == 1) {
 140                         $switch_sum++;
 141                         push @sum, $line;
 142                         if ($line =~ m/^Elapsed\stime:\s+/) {
 143                                 $sum = 0;
 144                         }
 145                 }
 146                 if ($motif == 1){
 147                         $switch++;
 148                                 if ($logo == 1 && $line !~ m/^\s+\*+/ ) {
 149                                         $switch_logo++;
 150                                         my @a = split(/\s+/,$line);
 151                                         print  $wl_out_fh ">seq_$switch_logo\n$a[5]\n";
 152                                         @aa = split(/\s+/,$line);
 153                                         print $motif_tab_fh "$line\n";
 154                                 }
 155                             if ($line =~ m/^Num\sMotifs/ ) {
 156                                     $logo = 1;
 157                                     open ($wl_out_fh, ">", $logo_file) || die ("\nERROR: the file $logo_file could not be found\n");
 158                                     push @motif_element, $logo_file;
 159                                     push @logofile_id, $lf_id;
 160                                     @motif_width = split (/,/,$widths_of_motifs);
 161                                     print "logo file ID: @logofile_id\n";
 162                                     print "motif lenght: @motif_width\n";
 163                                     open ($motif_tab_fh, ">", $motif_tab) || die ("\nERROR: the file $motif_tab could not be found\n");
 164                                     push @motif_table_file, $motif_tab;
 165                                 }
 166                             elsif ($line =~ m/^\s+\*+/ ) {
 167                                         $logo = 0;
 168                                         my ($fh, $filename) =tempfile("XXXXX", DIR => "$basePath/static/documents/tempfiles/motifs_finder/");
 169                                         #my ($fh, $filename) =tempfile("XXXXX", DIR => "$basePath/motifs_finder/");
 170                                 }
 171                                 if ($freq_tab == 1) {
 172                                         $freq_tab_switch++;
 173                                         print $freq_tab_fh "$line\n";
 174                                 }
 175                                 if ($line =~ m/^Motif\smodel/ ) {
 176                                         $freq_tab = 1;
 177                                         open ($freq_tab_fh, ">", $freq_tab_file) || die ("\nERROR: the file $freq_tab could not be found\n");
 178                                         push @freq_tab, $freq_tab_file;
 179                                         print "FREQ TABLE: $freq_tab[0]\n";
 180                                 }
 181                                 elsif ($line =~ m/^site\s+/ ) {
 182                                         $freq_tab = 0;
 183                                         my ($fh, $filename) =tempfile("XXXXX", DIR => "$basePath/static/documents/tempfiles/motifs_finder/");
 184                                         #my ($fh, $filename) =tempfile("XXXXX", DIR => "$basePath/motifs_finder/");
 185                                 }
 186                                 if ($prob_tab == 1 && $line !~ m/^Background\sprobability\smodel/) {
 187                                         $prob_tab_switch++;
 188                                         print $prob_tab_fh "$line\n";
 189                                 }
 190                                 if ($line =~ m/^Motif\sprobability\smodel/ ) {
 191                                         $prob_tab = 1;
 192                                         open ($prob_tab_fh, ">", $prob_tab_file) || die ("\nERROR: the file $prob_tab_file could not be found\n");
 193                                         push @prob_tab, $prob_tab_file;
 194                                 }
 195                                 elsif ($line =~ m/^Background\sprobability\smodel/ ) {
 196                                         $prob_tab = 0;
 197                                         #my ($fh, $filename) =tempfile("XXXXX", DIR => "$basePath/motifs_finder/");
 198                                         my ($fh, $filename) =tempfile("XXXXX", DIR => "$basePath/static/documents/tempfiles/motifs_finder/");
 199                                 }
 200                                 if ($BGPM_tab == 1) {
 201                                         $BGPM_tab_switch++;
 202                                         print $BGPM_tab_fh "$line\n";
 203                                 }
 204                                 if ($line =~ m/^Background\sprobability\smodel/ ) {
 205                                         $BGPM_tab = 1;
 206                                         open ($BGPM_tab_fh, ">", $BGPM_tab_file) || die ("\nERROR: the file $BGPM_tab_file could not be found\n");
 207                                         push @BGPM_tab, $BGPM_tab_file;
 208                                 }
 209                                 elsif ($line =~ m/^\s+\d\.\d+\s\d\.\d+\s/ ) {
 210                                         $BGPM_tab = 0;
 211                                         my ($fh, $filename) =tempfile("XXXXX", DIR => "$basePath/static/documents/tempfiles/motifs_finder/");
 212                                         #my ($fh, $filename) =tempfile("XXXXX", DIR => "$basePath/motifs_finder/");
 213                                 }
 214                                 if ($sum_indv_tab == 1 ) {
 215                                         $sum_indv_tab_switch++;
 216                                         print $sum_indv_tab_fh "$line\n";
 217                                         print "FREQ LINES: $line\n";
 218                                 }
 219                                 if ($line =~ m/^Column\s\d\s:\s+Sequence\sDescription\sfrom\s/ ) {
 220                                         $sum_indv_tab = 1;
 221                                         open ($sum_indv_tab_fh, ">", $sum_indv_tab_file) || die ("\nERROR: the file $sum_indv_tab_file could not be found\n");
 222                                         push @sum_indv_tab, $sum_indv_tab_file;
 223                                 }
 224                                 elsif ($line =~ m/^Log\sFragmentation\sportion\sof\sMAP\sfor\smotif\s/ ) {
 225                                         $sum_indv_tab = 0;
 226                                         my ($fh, $filename) =tempfile("XXXXX", DIR => "$basePath/static/documents/tempfiles/motifs_finder/");
 227                                         #my ($fh, $filename) =tempfile("XXXXX", DIR => "$basePath/motifs_finder/");
 228                                 }
 229                 }
 230                 if ($line =~ m/^\s+MOTIF\s+([a-z])/){
 231                         $motif = 1;
 232                         $logo_file = $filename."_".$1."_wl_input.fasta";
 233                         $lf_id = $1;
 234                         $motif_tab = $filename."_".$1;
 235                         $freq_tab_file = $filename."_freq_".$1;
 236                         $prob_tab_file = $filename."_prob_".$1;
 237                         $BGPM_tab_file = $filename."_BGPM_".$1;
 238                         $sum_indv_tab_file = $filename."_sum_indv_".$1;
 239                 }
 240                 elsif ($line =~ m/^Log\s+Fragmentation\s+portion\s+/ ) {
 241                                 $motif = 0;
 242                                 close $wl_out_fh;
 243                                 close $motif_tab_fh;
 244                                 close $freq_tab_fh;
 245                                 close $prob_tab_fh;
 246                                 close $BGPM_tab_fh;
 247                                 close $sum_indv_tab_fh;
 248                 }
 249           }
 250
 251           my @values_motif;
 252           my $motif_table_value;
 253           foreach $filename (@motif_table_file){
 254                 $motif_table_value = get_result_table($filename);
 255                 push @values_motif, $motif_table_value;
 256           }
 257           my $freq_tab_value;
 258           my @value_freq_tab;
 259           foreach $filename (@freq_tab) {
 260                 $freq_tab_value = get_freq_table($filename);
 261                 push @value_freq_tab, $freq_tab_value;
 262           }
 263           my $prob_tab_value;
 264           my @value_prob_tab;
 265
 266           foreach $filename (@prob_tab) {
 267                 $prob_tab_value = get_prob_table($filename);
 268                 push @value_prob_tab, $prob_tab_value;
 269           }
 270           my $BGPM_tab_value;
 271           my @value_BGPM_tab;
 272           foreach $filename (@BGPM_tab) {
 273             $BGPM_tab_value = get_BGPM_table($filename);
 274                 push @value_BGPM_tab, $BGPM_tab_value;
 275           }
 276           my $sum_indv_tab_value;
 277           my @value_sum_indv_tab;
 278           foreach $filename (@sum_indv_tab) {
 279                 $sum_indv_tab_value = get_sum_indv_table($filename);
 280                 push @value_sum_indv_tab, $sum_indv_tab_value;
 281           }
 282
 283         # To run weblogo
 284         my $cmd;
 285         foreach $filename (@motif_element){
 286                 $cmd = "$cluster_shared_bindir/weblogo/seqlogo -F PNG -d 0.5 -T 1 -b -e -B 2 -h 5 -w 18 -y bits -a -M -n -Y -c -f $filename -o ".$filename."_weblogo";
 287                 push (@logo_image, basename($filename."_weblogo.png"));
 288                 my $error = system($cmd);
 289         }
 290
 291         print STDERR Dumper(\@logo_image);
 292         $c->stash->{sum} = join("<br/>", @sum);
 293         $c->stash->{sum_indv_tab} = \@value_sum_indv_tab;
 294         $c->stash->{BGPM_tab} = \@value_BGPM_tab;
 295         $c->stash->{prob_tab} = \@value_prob_tab;
 296         $c->stash->{freq_tab} = \@value_freq_tab;
 297         $c->stash->{motif_tab} = \@values_motif;
 298         $c->stash->{tfile} = join("\n", @string_result);
 299         $c->stash->{res} = join("<br/>", @string_result);
 300         $c->stash->{outfile} = $filename."_output";
 301         $c->stash->{parameters} = "$sequence $widths_of_motifs $numbers_of_sites @string_result";
 302         $c->stash->{logo} = \@logo_image;
 303         $c->stash->{logoID} = \@logofile_id;
 304         $c->stash->{logowidth} = \@motif_width;
 305
 306         $c->stash->{template} = 'tools/motifs_finder/motif_output.mas';
 307     }
 308
 309
 310     sub download_file :Path('/result/') :Args(0) {
 311         my ($self, $c) = @_;
 312         my $params = $c->req->body_params();
 313         my $filename = $c->req->param("file_name");
 314         my $result_file = $c->req->param("output_file");
 315
 316         if ($result_file) {
 317                 $result_file =~ s/<br\/>/\n/gi;
 318         }
 319
 320         #----------------------------------- send file
 321         $c->res->content_type('text/plain');
 322         $c->res->header('Content-Disposition', qq[attachment; filename="$filename"]);
 323         $c->res->body($result_file);
 324         #$c->stash->{template} = '/output.mas';
 325     }
 326
 327     sub get_result_table {
 328         my $motif_table_file = shift;
 329         my $motif_table_path = $motif_table_file;
 330
 331         #print "MOTIF TAB1 PATH: $motif_table_path\n";
 332         open (my $tab_fh, "<", $motif_table_path) || die ("\nERROR: the file $motif_table_path could not be found\n");
 333         my $html_table .= "<div class='container'>\n";
 334         $html_table .=  "<table>\n";
 335         $html_table .= "<table class='table table-bordered' border=1 cellpadding=0>";
 336         $html_table .=  "<tr>\n";
 337         $html_table .= "<th>Seq Num</th>\t";
 338         $html_table .=  "<th>Site Num</th>\t";
 339         $html_table .=  "<th>Left Loc</th>\t";
 340         # $html_table .=  "<th></th>\t";
 341         $html_table .=  "<th>Motifs</th>\t";
 342         # $html_table .=  "<th></th>\t";
 343         $html_table .=  "<th>Right Loc</th>\t";
 344         $html_table .=  "<th>Motif Prob</th>\t";
 345         $html_table .=  "<th>F/R Motif</th>\t";
 346         $html_table .=  "    <th>Seq Desc</th>\t";
 347         $html_table .=  "  </tr>\n";
 348
 349         while (my $inpbuf = <$tab_fh>){
 350             chomp $inpbuf;
 351                 $inpbuf =~ s/,//g;
 352                 my ($kk,$seq_num,$site_num,$left_loc,$emty1,$motif,$emty2,$right_loc,$prob,$f_motif,$seq_desc) = split(/\s+/,$inpbuf);
 353             $html_table .=  "<tr>\n";
 354             $html_table .=  "<td>$seq_num</td>\t";
 355             $html_table .=  "<td>$site_num</td>\t";
 356             $html_table .=  "<td>$left_loc</td>\t";
 357             # $html_table .=  "<td>$emty1</td>\t";
 358                 $html_table .=  "<td>$motif</td>\t";
 359             # $html_table .=  "<td>$emty2</td>\t";
 360             $html_table .=  "<td>$right_loc</td>\t";
 361             $html_table .=  "<td>$prob</td>\t";
 362                 $html_table .=  "<td>$f_motif</td>\t";
 363             $html_table .=  "    <td>$seq_desc</td>\t";
 364             $html_table .=  "  </tr>\n";
 365         }
 366
 367         close $tab_fh;
 368         $html_table .=  "</table>\n";
 369         $html_table .= "</div>";
 370     }
 371
 372     sub get_freq_table {
 373         my $freq_tab = shift;
 374         my $freq_table_path = $freq_tab;
 375         open (my $tab_fh, "<", $freq_table_path) || die ("\nERROR: the file $freq_table_path could not be found\n");
 376         my $html_freq_table .= "<div class='container'>\n";
 377         $html_freq_table .=  "<table>\n";
 378         $html_freq_table .= "<table class='table table-bordered' border=1 cellpadding=0>";
 379         #$html_freq_table .= "<div id=prob>";
 380         #$html_freq_table .= "<table style=float:left>";
 381         $html_freq_table .=  "<tr>\n";
 382         $html_freq_table .= "<th>Position #</th>\t";
 383         $html_freq_table .= "<th>A</th>\t";
 384         $html_freq_table .= "<th>T</th>\t";
 385         $html_freq_table .= "<th>C</th>\t";
 386         $html_freq_table .= "<th>G</th>\t";
 387         $html_freq_table .= "<th>Info</th>\t";
 388         $html_freq_table .=  "</tr>\n";
 389
 390         while (my $inpbuf = <$tab_fh>){
 391             chomp $inpbuf;
 392                 $inpbuf =~ s/_//g;
 393                 $inpbuf =~ s/\|//g;
 394                 $inpbuf =~ s/^\s+//g;
 395                 if ($inpbuf =~ m/^\S+/ && $inpbuf !~ m/^Pos.\s+/){
 396                         my ($pos_num,$A,$T,$C,$G,$info,) = split(/\s+/,$inpbuf);
 397                         $html_freq_table .=  "<tr>\n";
 398                         $html_freq_table .= " <td>$pos_num</td>\t";
 399                         $html_freq_table .= " <td>$A</td>\t";
 400                         $html_freq_table .= " <td>$T</td>\t";
 401                         $html_freq_table .= " <td>$C</td>\t";
 402                         $html_freq_table .= " <td>$G</td>\t";
 403                         $html_freq_table .= " <td>$info</td>\t";
 404                         $html_freq_table .=  "  <tr>\n";
 405                 }
 406         }
 407
 408         close $tab_fh;
 409         $html_freq_table .=  "</table>\n";
 410         $html_freq_table .=  "</div>\n";
 411     }
 412
 413     sub get_prob_table {
 414         my $prob_tab = shift;
 415         my $prob_table_path = $prob_tab;
 416         open (my $tab_fh, "<", $prob_table_path) || die ("\nERROR: the file $prob_table_path could not be found\n");
 417         my $html_prob_table .= "<div class='container'>\n";
 418         $html_prob_table .=  "<table>\n";
 419         $html_prob_table .= "<table class='table table-bordered' border=1 cellpadding=0>";
 420         $html_prob_table .= "<div id=prob>";
 421         $html_prob_table .=  "<tr>\n";
 422         $html_prob_table .= "<th>Position #</th>\t";
 423         $html_prob_table .= "<th>A</th>\t";
 424         $html_prob_table .= "<th>T</th>\t";
 425         $html_prob_table .= "<th>C</th>\t";
 426         $html_prob_table .= "<th>G</th>\t";
 427         $html_prob_table .=  "</tr>\n";
 428
 429         while (my $inpbuf = <$tab_fh>){
 430             chomp $inpbuf;
 431                 $inpbuf =~ s/_//g;
 432                 $inpbuf =~ s/\|//g;
 433                 $inpbuf =~ s/^\s+//g;
 434                 if ($inpbuf =~ m/^\S+/ && $inpbuf !~ m/^Pos.\s+/){
 435                         #if ($inpbuf =~ m/^Background\sprobability\smodel/){
 436                                 #$inpbuf =~ s/\s//g;
 437                                 #$inpbuf =~ s/Backgroundprobabilitymodel/BP-Model/g;
 438                         #}
 439                         my ($pos_num,$A,$T,$C,$G) = split(/\s+/,$inpbuf);
 440                         $html_prob_table .=  "  <tr>\n";
 441                         $html_prob_table .= " <td>$pos_num</td>\t";
 442                         $html_prob_table .= " <td>$A</td>\t";
 443                         $html_prob_table .= " <td>$T</td>\t";
 444                         $html_prob_table .= " <td>$C</td>\t";
 445                         $html_prob_table .= " <td>$G</td>\t";
 446                         $html_prob_table .=  "  <tr>\n";
 447                 }
 448         }
 449
 450         close $tab_fh;
 451         $html_prob_table .=  "</table>\n";
 452         $html_prob_table .=  "</div>\n";
 453     }
 454
 455
 456     sub get_BGPM_table {
 457        my $BGPM_tab = shift;
 458        my $BGPM_table_path = $BGPM_tab;
 459        open (my $tab_fh, "<", $BGPM_table_path) || die ("\nERROR: the file $BGPM_table_path could not be found\n");
 460        my $html_BGPM_table .= "<div class='container'>\n";
 461        $html_BGPM_table .=  "<table style='width:100%'>\n";
 462        $html_BGPM_table .= "<table class='table table-bordered' border=1 cellpadding=0>";
 463        $html_BGPM_table .= "<thead>";
 464        $html_BGPM_table .=  " <tr>\n";
 465        $html_BGPM_table .= "<th style='width:10%'>A</th>\t";
 466        $html_BGPM_table .= " <th style='width:10%'>T</th>\t";
 467        $html_BGPM_table .= " <th style='width:10%'>C</th>\t";
 468        $html_BGPM_table .= " <th style='width:10%'>G</th>\t";
 469        $html_BGPM_table .=  " </tr>\n";
 470        $html_BGPM_table .=  " </thead>\n";
 471
 472         while (my $inpbuf = <$tab_fh>){
 473             chomp $inpbuf;
 474                 $inpbuf =~ s/^\s+//g;
 475                 my ($A,$T,$C,$G) = split(/\s+/,$inpbuf);
 476                 $html_BGPM_table .=  "<tbody>\n";
 477                 $html_BGPM_table .=  "<tr>\n";
 478                 $html_BGPM_table .= "<td>$A</td>\t";
 479                 $html_BGPM_table .= "<td>$T</td>\t";
 480                 $html_BGPM_table .= "<td>$C</td>\t";
 481                 $html_BGPM_table .= "<td>$G</td>\t";
 482                 $html_BGPM_table .=  "<tr>\n";
 483                 $html_BGPM_table .=  "</tbody>\n";
 484         }
 485
 486         close $tab_fh;
 487         $html_BGPM_table .=  "</table>\n";
 488         $html_BGPM_table .= "</div>";
 489     }
 490
 491     sub get_sum_indv_table {
 492         my $sum_indv_tab = shift;
 493         my $sum_indv_table_path = $sum_indv_tab;
 494         open (my $tab_fh, "<", $sum_indv_table_path) || die ("\nERROR: the file $sum_indv_table_path could not be found\n");
 495         my $html_sum_indv_table;
 496         while ( my $inpbuf = <$tab_fh>){
 497             chomp $inpbuf;
 498                 if ($inpbuf =~ m/^\S+/ ){
 499                         my $html_inpbuf = join("<br/>", $inpbuf);
 500                         $html_sum_indv_table .= "$html_inpbuf<br/>\n";
 501                 }
 502         }
 503
 504         close $tab_fh;
 505         $html_sum_indv_table;
 506     }
 507
 508 }
 509
 510 =encoding utf8
 511
 512 =head1 AUTHOR
 513
 514 Alex Ogbonna (aco46@cornell.edu)
 515
 516 =head1 LICENSE
 517
 518 This library is free software. You can redistribute it and/or modify
 519 it under the same terms as Perl itself.
 520
 521 =cut
 522
 523 __PACKAGE__->meta->make_immutable;
 524
 525 1;