lib/SGN/Controller/AJAX/SimSearch.pm

   1
   2 package SGN::Controller::AJAX::SimSearch;
   3
   4 use Moose;
   5 use File::Temp "tempdir";
   6 use File::Basename;
   7
   8 BEGIN { extends 'Catalyst::Controller::REST'; }
   9
  10
  11 __PACKAGE__->config(
  12     default   => 'application/json',
  13     stash_key => 'rest',
  14     map       => { 'application/json' => 'JSON' },
  15     );
  16
  17
  18
  19 sub process_file :Path('/ajax/tools/simsearch/process_file') :Args(0) {
  20     my $self = shift;
  21     my $c = shift;
  22
  23
  24     my $filename = $c->config->{basepath}."/".$c->config->{tempfiles_subdir}."/simsearch/".$c->req->param("filename");
  25     my $fileurl = '/simsearch/'.$c->req->param("filename");
  26     my $format = $c->req->param("format");
  27
  28     print STDERR "FORMAT = $format\n";
  29
  30 #    if ($format eq "vcf") {
  31 #       print STDERR "Converting vcf to dosage...\n";
  32 #       system("perl ../gtsimsrch/src/vcf2dosage.pl < $filename > $filename.dosage");
  33 #       $filename = $filename.".dosage";
  34  #   }
  35
  36
  37
  38     print STDERR "READING FROM $filename\n";
  39     my $reference_file = $c->req->param("reference_file");
  40
  41     my $reference_file_path = $c->config->{simsearch_datadir}."/".$reference_file;
  42     # do not specify -r option when there is no reference file
  43     #
  44     my $ref_option = "";
  45     if ($reference_file) {
  46         $ref_option = " -ref $reference_file_path ";
  47     }
  48
  49 #    my $cmd = "../gtsimsrch/src/simsearch -i $filename $ref_option -o $filename.out";
  50
  51     my $cmd = "../gtsimsrch/src/duplicate_finder.pl -alt_marker_ids -nofull_cluster_output -max_distance 0.5 -in $filename $ref_option -output $filename.out -graphics GD -histogram_filename $filename.out_distances_histogram.png -histogram_path /home/production/cxgn/gtsimsrch/src/histogram.pl";
  52     print STDERR "running command $cmd...\n";
  53     system($cmd);
  54
  55
  56     my $results;
  57     open(my $F , "<", $filename.".out_clusters") || die "Can't open file $filename.out_clusters";
  58
  59     my @data;
  60     my @line;
  61
  62     my $group =1;
  63
  64     print STDERR "Parsing output file...\n";
  65     while(<$F>) {
  66         print STDERR "Processing group $group...\n";
  67         chomp;
  68         if (/^#/) { next; }
  69         @line = split " ";
  70         my @members = @line[9..@line-1];
  71
  72         push @data, [ $group, $line[0], $line[3], $line[2], join("<br />", @members) ];
  73         $group++;
  74     }
  75     close($F);
  76     print STDERR "Done.\n";
  77
  78     # plot the agmr score distribution histogram using the 6th column in $filename.out
  79     #
  80     # (use gnuplot or R)
  81
  82     $c->stash->{rest} = { data => \@data,
  83                           histogram => '/documents/tempfiles/'.$fileurl.".out_distances_histogram.png"   };
  84
  85 }
  86
  87 1;
  88