lib/SGN/Controller/SimSearch.pm

   1
   2 package SGN::Controller::SimSearch;
   3
   4 use Moose;
   5 use File::Temp "tempdir";
   6 use File::Basename;
   7
   8 BEGIN { extends 'Catalyst::Controller'; }
   9
  10 sub simsearch : Path('/tools/simsearch') {
  11     my $self = shift;
  12     my $c = shift;
  13
  14     $c->stash->{template} = '/tools/simsearch/index.mas';
  15 }
  16
  17 sub upload_file : Path('/tools/simsearch/upload_file') {
  18     my $self = shift;
  19     my $c = shift;
  20
  21     my $tempdir = $c->tempfiles_subdir("simsearch");
  22     my $tempfile = $c->config->{basepath}."/".$c->tempfile( TEMPLATE => 'simsearch/simsearch-XXXXXX', UNLINK => 0 );
  23
  24
  25     my $upload = $c->request->upload('upload_vcf_file');
  26
  27     my $filename = $upload->filename();
  28
  29     print STDERR "UPLOAD FILENAME: $filename\n";
  30     my $format = "dosage";
  31
  32     if ($filename =~ m/\.vcf$/) {
  33         $format = "vcf";
  34     }
  35
  36     my $tempname = $upload->tempname();
  37     print STDERR "TEMPNAME: $tempname\n";
  38
  39     $c->stash->{filename} = $tempfile;
  40     $c->stash->{template} = '/tools/simsearch/upload_file.mas';
  41
  42     my $simsearch_datadir = $c->config->{simsearch_datadir};
  43
  44     print STDERR "SIMSEARCH DATADIR = $simsearch_datadir\n";
  45
  46     $upload->copy_to($tempfile);
  47
  48     my @files = glob "$simsearch_datadir/*";
  49
  50     print STDERR "FILES: ".join(",",@files)."\n";
  51
  52
  53
  54     my $pulldown = "<select id=\"reference_file\" >\n";
  55     foreach my $f (@files) {
  56         $pulldown .= "<option>".basename($f)."</option>";
  57     }
  58     $pulldown .="</select>";
  59
  60     # -i required input file -r reference file (with -i only, input is also used as reference)
  61     # need to add a pull down with current genotypes for each protocol
  62
  63     print STDERR "COPIED TO $tempfile\n";
  64     $c->stash->{reference_files_menu} = $pulldown;
  65     $c->stash->{filename} = basename($tempfile);
  66     $c->stash->{user_readable_filename} = basename($filename);
  67     $c->stash->{format} = $format;
  68 }
  69
  70 sub process_file :Path('/tools/simsearch/process_file') :Args(0) {
  71     my $self = shift;
  72     my $c = shift;
  73
  74     my $filename = $c->config->{basepath}."/".$c->config->{tempfiles_subdir}."/simsearch/".$c->req->param("filename");
  75
  76     my $fileurl = "/simsearch/".$c->req->param("filename");
  77
  78     print STDERR "READING FROM $filename\n";
  79     my $reference_file = $c->req->param("reference_file");
  80
  81     my $reference_file_path = $c->config->{simsearch_datadir}."/".$reference_file;
  82     # do not specify -r option when there is no reference file
  83     #
  84     my $ref_option = "";
  85     if ($reference_file) {
  86         $ref_option = " -r $reference_file_path ";
  87     }
  88
  89     my $cmd = "../gtsimsrch/src/simsearch -i $filename $ref_option -o $filename.out";
  90
  91     print STDERR "running command $cmd...\n";
  92     system($cmd);
  93
  94
  95     system("perl ../gtsimsrch/src/agmr_cluster.pl < $filename.out > $filename.out.clusters");
  96
  97     my $results;
  98     open(my $F , "<", $filename.".out.clusters") || die "Can't open file $filename.out";
  99
 100     my @line;
 101     my @data;
 102     my $html = "<table cellspacing=\"20\" cellpadding=\"20\" border=\"1\">";
 103     my $group =1;
 104     while(<$F>) {
 105         if (/^#/) { next; }
 106         @line = split /\s+/;
 107         $html .= '<tr><td>'.$group.'</td><td>'. join('<br />', @line[4..@line-1])."</td></tr>\n";
 108         $group++;
 109         push @data, \@line;
 110     }
 111     $html.="</table>\n";
 112     close($F);
 113
 114     # plot the agmr score distribution histogram using the 6th column in $filename.out
 115     #
 116     # (use gnuplot or R)
 117
 118     $c->stash->{results} = $html;
 119     $c->stash->{data} = \@data;
 120     $c->stash->{histogram} = $fileurl.".out_distances_histogram.png";
 121
 122
 123     $c->stash->{template} = '/tools/simsearch/results.mas';
 124
 125
 126 }
 127
 128 1;
 129