lib/SGN/Controller/AJAX/Blast.pm

   1
   2 package SGN::Controller::AJAX::Blast;
   3
   4 use Moose;
   5
   6 use Bio::SeqIO;
   7 use Config::Any;
   8 use Data::Dumper;
   9 use Storable qw | nstore retrieve |;
  10 use Try::Tiny;
  11 use Tie::UrlEncoder; our %urlencode;
  12 use File::Temp qw | tempfile |;
  13 use File::Basename qw | basename |;
  14 use File::Copy qw | copy |;
  15 use File::Spec qw | catfile |;
  16 use File::Slurp qw | read_file write_file |;
  17 use File::NFSLock qw | uncache |;
  18 use CXGN::Tools::Run;
  19 use CXGN::Page::UserPrefs;
  20 use CXGN::Tools::List qw/distinct evens/;
  21 use CXGN::Blast::Parse;
  22 use CXGN::Blast::SeqQuery;
  23
  24 use JSON::Any;
  25 my $json = JSON::Any->new;
  26
  27 use Time::HiRes qw(gettimeofday tv_interval);
  28
  29 BEGIN { extends 'Catalyst::Controller::REST'; };
  30
  31 __PACKAGE__->config(
  32     default   => 'application/json',
  33     stash_key => 'rest',
  34     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  35    );
  36
  37 sub run : Path('/tools/blast/run') Args(0) {
  38     my $self = shift;
  39     my $c = shift;
  40
  41     my $params = $c->req->params();
  42     my $input_query = CXGN::Blast::SeqQuery->new();
  43     my $valid = $input_query->validate($c, $params->{input_options}, $params->{sequence});
  44
  45     if ($valid ne "OK") {
  46       $c->stash->{rest} = { error => "Your input contains illegal characters. Please verify your input." };
  47       return;
  48     }
  49
  50     $params->{sequence} = $input_query->process($c, $params->{input_options}, $params->{sequence});
  51
  52         if ($params->{input_options} eq 'autodetect') {
  53                 my $detected_type = $input_query->autodetect_seq_type($c, $params->{input_options}, $params->{sequence});
  54
  55                 # print STDERR "SGN BLAST detected your sequence is: $detected_type\n";
  56
  57                 # create a hash with the valid options =1 and check and if result 0 return error
  58                 my %blast_seq_db_program = (
  59                         nucleotide => {
  60                                 nucleotide => {
  61                                         blastn => 1,
  62                                         tblastx => 1,
  63                                 },
  64                                 protein => {
  65                                         blastx => 1,
  66                                 },
  67                         },
  68                         protein => {
  69                                 protein => {
  70                                         blastp => 1,
  71                                 },
  72                                 nucleotide => {
  73                                         tblastn => 1,
  74                                 },
  75                         },
  76                 );
  77
  78                 if (!$blast_seq_db_program{$detected_type}{$params->{db_type}}{$params->{program}}) {
  79                         $c->stash->{rest} = { error => "the program ".$params->{program}." can not be used with a ".$detected_type." sequence (autodetected) and a ".$params->{db_type}." database.\n\nPlease, use different options and disable the autodetection of the query type if it is wrong." };
  80                         return;
  81                 }
  82         }
  83
  84     my $seq_count = 1;
  85     my $blast_tmp_output = $c->config->{cluster_shared_tempdir}."/blast";
  86     mkdir $blast_tmp_output if ! -d $blast_tmp_output;
  87     if ($params->{sequence} =~ /\>/) {
  88         $seq_count= $params->{sequence} =~ tr/\>/\>/;
  89     }
  90
  91     print STDERR "SEQ COUNT = $seq_count\n";
  92     my ($seq_fh, $seqfile) = tempfile(
  93       "blast_XXXXXX",
  94       DIR=> $blast_tmp_output,
  95     );
  96
  97     my $jobid = basename($seqfile);
  98
  99     print STDERR "JOB ID CREATED: $jobid\n";
 100
 101     my $schema = $c->dbic_schema("SGN::Schema");
 102
 103     my %arg_handlers =
 104         (
 105
 106          sequence =>
 107          sub {
 108              my $sequence = $params->{sequence};
 109               if( $sequence ) {
 110                  $sequence =~ s/^\s+|\s+$|\n\s*\n//g; #< trim out leading and trailing whitespace and blank lines
 111              #   if ($sequence !~ /^\s*>/) {
 112               #      $sequence = ">WEB-USER-SEQUENCE (Unknown)\n$sequence";
 113               #  }
 114               #  $sequence .= "\n"; #< add a final newline
 115
 116                  print STDERR "Opening file for sequence ($seqfile)... ";
 117                  open(my $FH, ">", $seqfile) || die "Can't open file for query ($seqfile)\n";
 118                  print $FH $sequence if $sequence;
 119                  close($FH);
 120
 121      # print STDERR "Done.\n";
 122
 123 #            if(my $file_upload = $page->get_upload) {
 124 #                if ( my $fh = $file_upload->fh ) {
 125 #                    print $seq_fh $_ while <$fh>;
 126 #                }
 127 #            }
 128
 129                  print STDERR "Parsing with bioperl... ";
 130                  my $i = Bio::SeqIO->new(
 131                      -format   => 'fasta',
 132                      -file       => $seqfile,
 133                      );
 134
 135                  try {
 136                      while ( my $s = $i->next_seq ) {
 137                          $s->length or $c->throw(
 138                              message  => 'Sequence '.encode_entities('"'.$s->id.'"').' is empty, this is not allowed by BLAST.',
 139                              is_error => 0,
 140                              );
 141                      }
 142                  } catch {
 143                      print STDERR $@;
 144                      die $_ if ref; #< throw it onward if it's an exception
 145                      my $full_error = $_;
 146                      if( /MSG:([^\n]+)/ ) {
 147                          $_ = $1;
 148                      }
 149                      s/at \/[\-\w \/\.]+ line \d+.+//; # remove anything resembling backtraces
 150                      $c->throw( message  => $_,
 151                                 is_error => 0,
 152                                 developer_message => $full_error,
 153                          );
 154                  };
 155
 156                  $seq_count >= 1 or $c->throw( message => 'no sequence submitted, cannot run BLAST',
 157                                                is_error => 0,
 158                                                developer_message => Data::Dumper::Dumper({
 159                                                    '$seq_count' => $seq_count,
 160                                                    '$seq_filename' => $seqfile,
 161                                                         }),
 162                 );
 163
 164                 return -i => $seqfile;
 165               }
 166          },
 167
 168          matrix =>
 169          sub {
 170              my $m = $params->{matrix};
 171              $m =~ /^(BLOSUM|PAM)\d+$/
 172                  or $c->throw( is_error => 0, message => "invalid matrix '$m'" );
 173              return -M => $m;
 174          },
 175
 176
 177          expect =>
 178          sub {
 179              $params->{evalue} =~ s/[^\d\.e\-\+]//gi; #can only be these characters
 180              return -e =>  $params->{evalue} ? $params->{evalue} : 1;
 181          },
 182
 183          maxhits =>
 184          sub {
 185              my $h = $params->{maxhits} || 20;
 186              $h =~ s/\D//g; #only digits allowed
 187              return -b => $h;
 188          },
 189
 190          hits_list =>
 191          sub {
 192              my $h = $params->{maxhits} || 20;
 193              $h =~ s/\D//g; #only digits allowed
 194              return -v => $h;
 195          },
 196
 197          filterq =>
 198          sub {
 199              return -F => $params->{filterq} ? 'T' : 'F';
 200          },
 201
 202          # outformat =>
 203          # sub {
 204          #     $params->{outformat} =~ s/\D//g; #only digits allowed
 205          #     return -m => $params->{outformat};
 206          # },
 207
 208          database =>
 209
 210          sub {
 211              my $bdb = $schema->resultset("BlastDb")->find($params->{database} )
 212                  or die "could not find bdb with file_base '$params->{database}'";
 213
 214              my $basename = File::Spec->catfile($c->config->{blast_db_path},$bdb->file_base());
 215              #returns '/data/shared/blast/databases/genbank/nr'
 216              #remember the ID of the blast db the user just blasted with
 217
 218              return -d => $basename;
 219          },
 220
 221          program =>
 222          sub {
 223              $params->{program} =~ s/[^a-z]//g; #only lower-case letters
 224              return -p => $params->{program};
 225          },
 226         );
 227
 228     print STDERR "BUILDING COMMAND...\n";
 229
 230
 231     # build our command with our arg handlers
 232     #
 233     my @command = ('blastall');
 234     foreach my $k (keys %arg_handlers) {
 235
 236       print STDERR "evaluating $k...";
 237       my @x = $arg_handlers{$k}->();
 238       print STDERR "component:
 239       ", (join ",", @x)."\n";
 240       @command = (@command, @x);
 241     }
 242
 243     # To get the proper format for gi sequences (CitrusGreening.org case)
 244     push(@command, '-I');
 245     push(@command, 'T');
 246
 247     print STDERR "COMMAND: ".join(" ", @command);
 248     print STDERR "\n";
 249
 250     # save our prefs
 251     # $prefs->save;
 252
 253     # now run the blast
 254     #
 255
 256
 257     my $job;
 258     eval {
 259       $job = CXGN::Tools::Run->run_cluster(
 260         @command,
 261         {
 262           temp_base => $blast_tmp_output,
 263           queue => $c->config->{'web_cluster_queue'},
 264           working_dir => $blast_tmp_output,
 265
 266           # temp_base => $c->config->{'cluster_shared_tempdir'},
 267           # queue => $c->config->{'web_cluster_queue'},
 268           # working_dir => $c->config->{'cluster_shared_tempdir'},
 269
 270                     # don't block and wait if the cluster looks full
 271                     max_cluster_jobs => 1_000_000_000,
 272             }
 273           );
 274
 275       print STDERR "Saving job state to $seqfile.job for id ".$job->job_id()."\n";
 276
 277       $job->do_not_cleanup(1);
 278
 279       nstore( $job, $seqfile.".job" ) or die 'could not serialize job object';
 280
 281     };
 282
 283
 284
 285     if ($@) {
 286       print STDERR "An error occurred! $@\n";
 287       $c->stash->{rest} = { error => $@ };
 288     }
 289     else {
 290                 # write data in blast.log
 291                 my $blast_log_path = $c->config->{blast_log};
 292                 my $blast_log_fh;
 293                 if (-e $blast_log_path) {
 294                         open($blast_log_fh, ">>", $blast_log_path) || print STDERR "cannot create $blast_log_path\n";
 295                 } else {
 296                         open($blast_log_fh, ">", $blast_log_path) || print STDERR "cannot open $blast_log_path\n";
 297                         print $blast_log_fh "Seq_num\tDB_id\tProgram\teval\tMaxHits\tMatrix\tDate\n";
 298                 }
 299                 print $blast_log_fh "$seq_count\t".$params->{database}."\t".$params->{program}."\t".$params->{evalue}."\t".$params->{maxhits}."\t".$params->{matrix}."\t".localtime()."\n";
 300
 301
 302                 print STDERR "Passing jobid code ".(basename($jobid))."\n";
 303                 $c->stash->{rest} = { jobid =>  basename($jobid),
 304                               seq_count => $seq_count,
 305                 };
 306     }
 307 }
 308
 309
 310 sub check : Path('/tools/blast/check') Args(1) {
 311     my $self = shift;
 312     my $c = shift;
 313     my $jobid = shift;
 314
 315     # my $t0 = [gettimeofday]; #-------------------------- TIME CHECK
 316
 317     my $blast_tmp_output = $c->get_conf('cluster_shared_tempdir')."/blast";
 318
 319     #my $jobid =~ s/\.\.//g; # prevent hacks
 320     my $job = retrieve($blast_tmp_output."/".$jobid.".job");
 321     if ( $job->alive ){
 322       # my $t1 = [gettimeofday]; #-------------------------- TIME CHECK
 323
 324       sleep(1);
 325       $c->stash->{rest} = { status => 'running', };
 326
 327       #       my $t2 = [gettimeofday]; #-------------------------- TIME CHECK
 328       #
 329       # my $t1_t2 = tv_interval $t1, $t2;
 330       #       print STDERR "Job alive: $t1_t2\n";
 331
 332       return;
 333     }
 334     else {
 335
 336       # my $t3 = [gettimeofday]; #-------------------------- TIME CHECK
 337
 338       # the job has finished
 339       # copy the cluster temp file back into "apache space"
 340       #
 341       my $result_file = $self->jobid_to_file($c, $jobid.".out");
 342
 343       my $job_out_file = $job->out_file();
 344       for( 1..10 ) {
 345             uncache($job_out_file);
 346             last if -f $job_out_file;
 347             sleep 1;
 348         #         my $t4 = [gettimeofday]; #-------------------------- TIME CHECK
 349         # my $t3_t4 = tv_interval $t3, $t4;
 350         #         print STDERR "Job not alive loop: $t3_t4\n";
 351
 352       }
 353       # my $t5 = [gettimeofday]; #-------------------------- TIME CHECK
 354
 355       -f $job_out_file or die "job output file ($job_out_file) doesn't exist";
 356       -r $job_out_file or die "job output file ($job_out_file) not readable";
 357
 358       # my $t6 = [gettimeofday]; #-------------------------- TIME CHECK
 359
 360       # You may wish to provide a different output file to send back
 361       # rather than STDOUT from the job.  Use the out_file_override
 362       # parameter if this is the case.
 363       #my $out_file = $out_file_override || $job->out_file();
 364       # system("ls $blast_tmp_output 2>&1 >/dev/null");
 365
 366       # my $t7 = [gettimeofday]; #-------------------------- TIME CHECK
 367
 368       # system("ls $c->{config}->{cluster_shared_tempdir} 2>&1 >/dev/null");
 369       copy($job_out_file, $result_file) or die "Can't copy result file '$job_out_file' to $result_file ($!)";
 370
 371       # my $t8 = [gettimeofday]; #-------------------------- TIME CHECK
 372
 373         #clean up the job tempfiles
 374         $job->cleanup();
 375
 376       # my $t9 = [gettimeofday]; #-------------------------- TIME CHECK
 377
 378         #also delete the job file
 379
 380       #       my $t10 = [gettimeofday]; #-------------------------- TIME CHECK
 381       #
 382       # my $t5_t6 = tv_interval $t5, $t6;
 383       # my $t6_t7 = tv_interval $t6, $t7;
 384       # my $t7_t8 = tv_interval $t7, $t8;
 385       # my $t8_t9 = tv_interval $t8, $t9;
 386       # my $t9_t10 = tv_interval $t9, $t10;
 387       #
 388       # my $t3_t10 = tv_interval $t3, $t10;
 389       # my $t0_t10 = tv_interval $t0, $t10;
 390       #
 391       #       print STDERR "check 5-6 interval: $t5_t6\n";
 392       #       print STDERR "check 6-7 interval: $t6_t7\n";
 393       #       print STDERR "check 7-8 interval: $t7_t8\n";
 394       #       print STDERR "check 8-9 interval: $t8_t9\n";
 395       #       print STDERR "check 9-10 interval: $t9_t10\n";
 396       #
 397       #       print STDERR "Job not alive (else): $t3_t10\n";
 398       #       print STDERR "CHECK SUB TIME: $t0_t10\n";
 399
 400
 401         $c->stash->{rest} = { status => "complete" };
 402     }
 403 }
 404
 405 # fetch some html/js required for displaying the parse report
 406 # sub get_prereqs : Path('/tools/blast/prereqs') Args(1) {
 407 #     my $self = shift;
 408 #     my $c = shift;
 409 #     my $jobid = shift;
 410
 411 #     my $format=$c->req->param('format');
 412 #     my $parser = CXGN::Blast::Parse->new();
 413 #     my $prereqs = $parser->prereqs($format);
 414 #     $c->stash->{rest} = { prereqs => $prereqs };
 415 # }
 416
 417 sub get_result : Path('/tools/blast/result') Args(1) {
 418     my $self = shift;
 419     my $c = shift;
 420     my $jobid = shift;
 421
 422     # my $t0 = [gettimeofday]; #-------------------------- TIME CHECK
 423
 424     my $format = $c->req->param('format');
 425     my $db_id = $c->req->param('db_id');
 426
 427     my $result_file = $self->jobid_to_file($c, $jobid.".out");
 428     my $blast_tmp_output = $c->get_conf('cluster_shared_tempdir')."/blast";
 429
 430     # system("ls $blast_tmp_output 2>&1 >/dev/null");
 431     # system("ls ".($c->config->{cluster_shared_tempdir})." 2>&1 >/dev/null");
 432
 433     my $schema = $c->dbic_schema("SGN::Schema");
 434     my $db = $schema->resultset("BlastDb")->find($db_id);
 435     if (!$db) { die "Can't find database with id $db_id"; }
 436     my $parser = CXGN::Blast::Parse->new();
 437     my $parsed_data = $parser->parse($c, $format, $result_file, $db);
 438
 439     # my $t1 = [gettimeofday]; #-------------------------- TIME CHECK
 440     # my $t0_t1 = tv_interval $t0, $t1;
 441     # print STDERR "GET RESULT SUB TIME: $t0_t1\n";
 442
 443     $c->stash->{rest} = $parsed_data; # { blast_report => '<pre>'.(join("\n", read_file($parsed_file))).'</pre>', };
 444 }
 445
 446
 447
 448
 449 sub render_canvas_graph : Path('/tools/blast/render_graph') Args(1) {
 450     my $self = shift;
 451     my $c = shift;
 452     my $jobid = shift;
 453     my $db_id = $c->req->param('db_id');
 454
 455     my $file = $self->jobid_to_file($c, $jobid.".out");
 456     my $blast_tmp_output = $c->get_conf('cluster_shared_tempdir')."/blast";
 457
 458     my $schema = $c->dbic_schema("SGN::Schema");
 459     my $bdb = $schema->resultset("BlastDb")->find($db_id);
 460     if (!$bdb) { die "Can't find database with id $db_id"; }
 461
 462
 463     my $jbrowse_path = $c->config->{jbrowse_path};;
 464     # my $db_id = $bdb->blast_db_id();
 465     my $jbr_src = $bdb->jbrowse_src();
 466
 467     my $query = "";
 468     my $subject = "";
 469     my $id = 0.0;
 470     my $aln = 0;
 471     my $qstart = 0;
 472     my $qend = 0;
 473     my $sstart = 0;
 474     my $send = 0;
 475     my $evalue = 0.0;
 476     my $score = 0;
 477     my $desc = "";
 478
 479     my $one_hsp = 0;
 480     my $start_aln = 0;
 481     my $append_desc = 0;
 482     my $query_line_on = 0;
 483     my $query_length = 0;
 484
 485     my @res_html;
 486     my @aln_html;
 487     push(@aln_html, "<br><pre>");
 488
 489     # variables for the canvas graph
 490     my @json_array;
 491
 492     open (my $blast_fh, "<", $file);
 493
 494     push(@res_html, "<table id=\"blast_table\" class=\"table\">");
 495     push(@res_html, "<tr><th>SubjectId</th><th>id%</th><th>Aln</th><th>evalue</th><th>Score</th><th>Description</th></tr>");
 496
 497     while (my $line = <$blast_fh>) {
 498       chomp($line);
 499
 500       if ($line =~ /Query\=\s*(\S+)/) {
 501         $query = $1;
 502         unshift(@res_html, "<center><h3>".$query." vs ".$bdb->title()."</h3></center>");
 503         $query_line_on = 1;
 504       }
 505
 506       if ($query_line_on && $line =~ /\((\d+)\s+letters/) {
 507         $query_length = $1;
 508       }
 509
 510       if ($append_desc) {
 511         if ($line =~ /\w+/) {
 512           my $new_desc_line = $line;
 513           $new_desc_line =~ s/\s+/ /g;
 514           $desc .= $new_desc_line;
 515         }
 516         else {
 517           $append_desc = 0;
 518         }
 519       }
 520
 521       if ($line =~ /^>/) {
 522         $start_aln = 1;
 523         $append_desc = 1;
 524
 525         if ($subject) {
 526           my $jbrowse_url = _build_jbrowse_url($jbr_src,$subject,$sstart,$send,$jbrowse_path);
 527           ($sstart,$send) = _check_coordinates($sstart,$send);
 528
 529           push(@res_html, "<tr><td><a id=\"$subject\" class=\"blast_match_ident\" href=\"/tools/blast/show_match_seq.pl?blast_db_id=$db_id;id=$subject;hilite_coords=$sstart-$send\" onclick=\"return resolve_blast_ident( '$subject', '$jbrowse_url', '/tools/blast/show_match_seq.pl?blast_db_id=$db_id;id=$subject;hilite_coords=$sstart-$send', null )\">$subject</a></td><td>$id</td><td>$aln</td><td>$evalue</td><td>$score</td><td>$desc</td></tr>");
 530
 531           if (length($desc) > 150) {
 532             $desc = substr($desc,0,150)." ...";
 533           }
 534
 535           my %description_hash;
 536
 537           $description_hash{"name"} = $subject;
 538           $description_hash{"id_percent"} = $id;
 539           $description_hash{"score"} = $score;
 540           $description_hash{"description"} = $desc;
 541           $description_hash{"qstart"} = $qstart;
 542           $description_hash{"qend"} = $qend;
 543           push(@json_array, \%description_hash);
 544
 545         }
 546         $subject = "";
 547         $id = 0.0;
 548         $aln = 0;
 549         $qstart = 0;
 550         $qend = 0;
 551         $sstart = 0;
 552         $send = 0;
 553         $evalue = 0.0;
 554         $score = 0;
 555         $desc = "";
 556         $one_hsp = 0;
 557
 558         if ($line =~ /^>(\S+)\s*(.*)/) {
 559           $subject = $1;
 560           $desc = $2;
 561
 562           # print STDERR "subject: $subject\n";
 563         }
 564       }
 565
 566
 567       if ($line =~ /Score\s*=/ && $one_hsp == 1) {
 568         my $jbrowse_url = _build_jbrowse_url($jbr_src,$subject,$sstart,$send,$jbrowse_path);
 569         ($sstart,$send) = _check_coordinates($sstart,$send);
 570
 571         push(@res_html, "<tr><td><a id=\"$subject\" class=\"blast_match_ident\" href=\"/tools/blast/show_match_seq.pl?blast_db_id=$db_id;id=$subject;hilite_coords=$sstart-$send\" onclick=\"return resolve_blast_ident( '$subject', '$jbrowse_url', '/tools/blast/show_match_seq.pl?blast_db_id=$db_id;id=$subject;hilite_coords=$sstart-$send', null )\">$subject</a></td><td>$id</td><td>$aln</td><td>$evalue</td><td>$score</td><td>$desc</td></tr>");
 572
 573         if (length($desc) > 150) {
 574           $desc = substr($desc,0,150)." ...";
 575         }
 576
 577         my %description_hash;
 578
 579         $description_hash{"name"} = $subject;
 580         $description_hash{"id_percent"} = $id;
 581         $description_hash{"score"} = $score;
 582         $description_hash{"description"} = $desc;
 583         $description_hash{"qstart"} = $qstart;
 584         $description_hash{"qend"} = $qend;
 585         push(@json_array, \%description_hash);
 586
 587         $id = 0.0;
 588         $aln = 0;
 589         $qstart = 0;
 590         $qend = 0;
 591         $sstart = 0;
 592         $send = 0;
 593         $evalue = 0.0;
 594         $score = 0;
 595       }
 596
 597       if ($line =~ /Score\s*=\s*([\d\.]+)/) {
 598         $score = $1;
 599         $one_hsp = 1;
 600         $append_desc = 0;
 601       }
 602
 603
 604       if ($line =~ /Expect\s*=\s*([\d\.\-e]+)/) {
 605         $evalue = $1;
 606       }
 607
 608       if ($line =~ /Identities\s*=\s*(\d+)\/(\d+)/) {
 609         my $aln_matched = $1;
 610         my $aln_total = $2;
 611         $aln = "$aln_matched/$aln_total";
 612         $id = sprintf("%.2f", $aln_matched*100/$aln_total);
 613       }
 614
 615       if (($line =~ /^Query:\s+(\d+)/) && ($qstart == 0)) {
 616         $qstart = $1;
 617       }
 618       if (($line =~ /^Sbjct:\s+(\d+)/) && ($sstart == 0)) {
 619         $sstart = $1;
 620       }
 621
 622       if (($line =~ /^Query:/) && ($line =~ /(\d+)\s*$/)) {
 623         $qend = $1;
 624       }
 625       if (($line =~ /^Sbjct:/) && ($line =~ /(\d+)\s*$/)) {
 626         $send = $1;
 627       }
 628
 629       if ($start_aln) {
 630         push(@aln_html, $line);
 631       }
 632
 633
 634     } # while_end
 635
 636
 637     my $jbrowse_url = _build_jbrowse_url($jbr_src,$subject,$sstart,$send,$jbrowse_path);
 638     ($sstart,$send) = _check_coordinates($sstart,$send);
 639
 640     push(@res_html, "<tr><td><a id=\"$subject\" class=\"blast_match_ident\" href=\"/tools/blast/show_match_seq.pl?blast_db_id=$db_id;id=$subject;hilite_coords=$sstart-$send\" onclick=\"return resolve_blast_ident( '$subject', '$jbrowse_url', '/tools/blast/show_match_seq.pl?blast_db_id=$db_id;id=$subject;hilite_coords=$sstart-$send', null )\">$subject</a></td><td>$id</td><td>$aln</td><td>$evalue</td><td>$score</td><td>$desc</td></tr>");
 641     push(@res_html, "</table>");
 642
 643
 644
 645     if (length($desc) > 150) {
 646       $desc = substr($desc,0,150)." ...";
 647     }
 648
 649     my %description_hash;
 650
 651     $description_hash{"name"} = $subject;
 652     $description_hash{"id_percent"} = $id;
 653     $description_hash{"score"} = $score;
 654     $description_hash{"description"} = $desc;
 655     $description_hash{"qstart"} = $qstart;
 656     $description_hash{"qend"} = $qend;
 657     push(@json_array, \%description_hash);
 658
 659
 660
 661
 662     my $prereqs = <<EOJS;
 663
 664         <div class="modal fade" id="xref_menu_popup" role="dialog">
 665           <div class="modal-dialog">
 666
 667             <!-- Modal content-->
 668             <div class="modal-content">
 669               <div class="modal-header">
 670                 <button type="button" class="close" data-dismiss="modal">&times;</button>
 671                 <h4 id="match_name" class="modal-title">Match Information</h4>
 672               </div>
 673               <div class="modal-body">
 674                 <dl>
 675                     <dd>
 676                       <div style="margin: 0.5em 0"><a class="match_details" href="" target="_blank">View matched sequence</a></div>
 677                       <div id="jbrowse_div" style="display:none"><a id="jbrowse_link" href="" target="_blank">View in genome context</a></div>
 678                     </dd>
 679                     <dd class="subject_sequence_xrefs">
 680                     </dd>
 681                 </dl>
 682               </div>
 683             </div>
 684
 685           </div>
 686         </div>
 687
 688
 689         <script>
 690           function resolve_blast_ident( id, jbrowse_url, match_detail_url, identifier_url ) {
 691
 692             var popup = jQuery( "#xref_menu_popup" );
 693
 694             jQuery('#match_name').html( id );
 695
 696             popup.find('a.match_details').attr( 'href', match_detail_url );
 697             popup.find('#jbrowse_link').attr( 'href', jbrowse_url );
 698
 699             if (jbrowse_url) {
 700               popup.find('#jbrowse_div').css( 'display', 'inline' );
 701             }
 702
 703             // look up xrefs for overall subject sequence
 704             var subj = popup.find('.subject_sequence_xrefs');
 705
 706             subj.html( '<img src="/img/throbber.gif" /> searching ...' );
 707             subj.load( '/api/v1/feature_xrefs?q='+id );
 708
 709             popup.modal("show");
 710
 711             return false;
 712           }
 713         </script>
 714
 715 EOJS
 716
 717
 718   push(@aln_html, "</pre></div><br>");
 719   my $blast_table = join('', @res_html);
 720   my $aln_text = join('<br>', @aln_html);
 721
 722
 723   $c->stash->{rest} = {
 724     sgn_html => $blast_table."<br>".$aln_text,
 725     desc_array => \@json_array,
 726     sequence_length => $query_length,
 727     prereqs => $prereqs
 728   };
 729
 730 }
 731
 732
 733
 734
 735 sub _build_jbrowse_url {
 736   my $jbr_src = shift;
 737   my $subject = shift;
 738   my $sstart = shift;
 739   my $send = shift;
 740   my $jbrowse_path = shift;
 741
 742   my $jbrowse_url = "";
 743
 744   if ($jbr_src) {
 745     if ($jbr_src =~ /(.+)_gene/) {
 746       $jbrowse_url = $jbrowse_path."/".$1."&loc=".$subject."&tracks=DNA,gene_models";
 747     }
 748     elsif ($jbr_src =~ /(.+)_genome/) {
 749       $jbrowse_url = $jbrowse_path."/".$1."&loc=".$subject."%3A".$sstart."..".$send."&tracks=DNA,gene_models";
 750     }
 751   }
 752
 753   return $jbrowse_url;
 754 }
 755
 756 sub _check_coordinates {
 757   my $tmp_start = shift;
 758   my $tmp_end = shift;
 759
 760   my $final_start = $tmp_start;
 761   my $final_end = $tmp_end;
 762
 763   if ($tmp_start > $tmp_end) {
 764     $final_start = $tmp_end;
 765     $final_end = $tmp_start;
 766   }
 767
 768   return ($final_start, $final_end);
 769 }
 770
 771
 772
 773
 774
 775
 776
 777
 778
 779
 780
 781
 782
 783
 784
 785
 786
 787 sub jobid_to_file {
 788     my $self = shift;
 789     my $c = shift;
 790     my $jobid = shift;
 791     return File::Spec->catfile($c->config->{basepath}, $c->tempfiles_subdir('blast'), "$jobid");
 792
 793 }
 794
 795 sub search_gene_ids {
 796         my $ids_array = shift;
 797         my $blastdb_path = shift;
 798         my @ids = @{$ids_array};
 799         my @output_seqs;
 800
 801         my $fs = Bio::BLAST::Database->open(full_file_basename => "$blastdb_path",);
 802
 803         foreach my $input_string (@ids) {
 804
 805                 if ($fs->get_sequence($input_string)) {
 806                         my $seq_obj = $fs->get_sequence($input_string);
 807                         my $seq = $seq_obj->seq();
 808                         my $id = $seq_obj->id();
 809                         my $desc = $seq_obj->desc();
 810                         my $new_seq = "";
 811
 812                         for (my $i=0; $i<length($seq); $i=$i+60) {
 813                                 $new_seq = $new_seq.substr($seq,$i,60)."<br>";
 814                         }
 815
 816                         push(@output_seqs, ">$id $desc<br>$new_seq");
 817                 }
 818         }
 819         return join('', @output_seqs);
 820 }
 821
 822 sub search_desc : Path('/tools/blast/desc_search/') Args(0) {
 823     my $self = shift;
 824     my $c = shift;
 825
 826     my @ids;
 827     my $schema = $c->dbic_schema("SGN::Schema");
 828     my $params = $c->req->params();
 829     my $input_string = $params->{blast_desc};
 830     my $db_id = $params->{database};
 831
 832     my $bdb = $schema->resultset("BlastDb")->find($db_id) || die "could not find bdb with file_base $db_id";
 833     my $blastdb_path = File::Spec->catfile($c->config->{blast_db_path}, $bdb->file_base());
 834
 835     my $grepcmd = "grep -i \"$input_string\" $blastdb_path \| sed 's/>//' \| cut -d ' ' -f 1";
 836     my $output_seq = `$grepcmd`;
 837     my $output_seqs;
 838
 839     if ($output_seq) {
 840       @ids = split(/\n/, $output_seq);
 841       $output_seqs = search_gene_ids(\@ids,$blastdb_path);
 842     }
 843     else {
 844       $output_seqs = "There were not results for your search\n";
 845     }
 846     $c->stash->{rest} = {output_seq => "$output_seqs"};
 847 }
 848
 849 1;