cgi-bin/tools/vector/index.pl

   1
   2 use strict;
   3 use warnings;
   4
   5 use File::Temp qw/tempfile/;
   6 use File::Basename;
   7 use File::Spec;
   8 use File::Slurp qw/slurp/;
   9
  10 use Bio::Seq;
  11 use Bio::Restriction::Analysis;
  12
  13 use CXGN::Page;
  14 use CXGN::Page::FormattingHelpers qw | info_section_html  html_break_string |;
  15 use CXGN::Cview::MapImage;
  16 use CXGN::Cview::Chromosome::Vector;
  17 use CXGN::Cview::Marker::VectorFeature;
  18 use CXGN::Tools::WebImageCache;
  19 use CXGN::Cview::VectorViewer;
  20 use CatalystX::GlobalContext '$c';
  21 ###############################################################################
  22
  23 my $p = CXGN::Page->new("Vector drawing application", "VeDraw");
  24 my ($action, $format, $name, $insert_sequence, $insert_coord, $show_re, $del_start ,$del_end, $native_file, $edit_commands) = $p->get_arguments("action", "format", "name" , "insert_sequence", "insert_coord", "show_re", "del_start", "del_end", "native_file", "edit_commands");
  25
  26 ###############################################################################
  27
  28
  29 our $native_commands;
  30
  31 #getting the file and url
  32 our $tempfiles_subdir_rel = File::Spec->catdir($c->config->{'tempfiles_subdir'},'cview'); #path relative to website root dir
  33 our $tempfiles_subdir_abs = File::Spec->catdir($c->config->{'basepath'},$tempfiles_subdir_rel); #absolute path
  34
  35 if ($native_file){
  36
  37     my $native_file_dir  = File::Spec->catfile($tempfiles_subdir_abs, $native_file);
  38     my $native_file_url   = File::Spec->catfile($tempfiles_subdir_rel, $native_file);
  39
  40     $native_commands = slurp ($native_file_dir);
  41 }
  42
  43 if (!$action) {
  44     display_form($p);
  45     exit();
  46 }
  47
  48 my $upload;
  49 my $data;
  50 my $size;
  51 my $s;
  52 my $seq;
  53 my $length;
  54 my @features;
  55 my @commands = ();
  56
  57 my @input_errors = (); #to collect validation errors
  58
  59 my $image_width = 800;
  60 my $image_height = 600;
  61 my $vv = CXGN::Cview::VectorViewer->new($name? $name : "vector", $image_width, $image_height);
  62
  63 if ($action eq "upload") {
  64
  65     $upload = $p->get_upload();
  66     if (!$upload) { die "NO UPLOAD OBJ"; }
  67     else {
  68         my $size = $upload->slurp($data);
  69         my $fh = $upload->fh;
  70
  71         if ($format eq "genbank") {
  72                 $vv->parse_genbank($fh);
  73         }
  74         elsif ($format eq "native") {
  75             my @lines = split /\n/, $data;
  76                 $vv->parse_native(@lines);
  77         }
  78
  79     }
  80 }
  81
  82
  83 elsif ($action eq "draw_native") {
  84     my @lines = split /\n/ms, $edit_commands;
  85     $vv->parse_native(@lines);
  86 }
  87 ###############################################################################
  88 if ($action eq "insert") {
  89
  90     my @lines = split /\n/ms, $native_commands;
  91     $vv->parse_native(@lines);
  92     $seq = $vv->get_sequence;
  93
  94      chomp($seq);
  95      my $preceding_seq =  substr($seq, 0, $insert_coord);
  96      my $following_seq =  substr($seq, $insert_coord +1, length($seq));
  97
  98      $seq = $preceding_seq . $insert_sequence . $following_seq;
  99
 100      $vv->set_sequence($seq);
 101      @commands = @{$vv->get_commands_ref};
 102      foreach my $c (@commands) {
 103          if ($c->[0] eq "SEQUENCE") {
 104              $c->[1]=$seq;
 105          }
 106      }
 107      $vv->set_commands_ref( \@commands);
 108      #$vv->parse_native();
 109
 110  }
 111 ###############################################################################
 112 if ($action eq "delete")  {
 113  my @lines = split /\n/ms, $native_commands;
 114     $vv->parse_native(@lines);
 115     $seq = $vv->get_sequence;
 116
 117      chomp($seq);
 118  my $seq_before = substr ($seq, 0 , $del_start);
 119  my $seq_after = substr ($seq , $del_end , length($seq));
 120  $seq = $seq_before . $seq_after;
 121  $vv->set_sequence($seq);
 122      @commands = @{$vv->get_commands_ref};
 123      foreach my $c (@commands) {
 124          if ($c->[0] eq "SEQUENCE") {
 125              $c->[1]=$seq;
 126          }
 127      }
 128      $vv->set_commands_ref( \@commands);
 129
 130 }
 131 ###############################################################################
 132 if ($action ne "draw_native") {
 133
 134     $vv->restriction_analysis($show_re);
 135 }
 136 ###############################################################################
 137
 138 my $image_html = $vv->generate_image();
 139 my $commands_ref = $vv->get_commands_ref();
 140 $seq = $vv->get_sequence();
 141
 142 ################################################################################
 143 #making temp file for the native format
 144 my $native_format_tempdir = File::Spec->catdir($c->config->{'basepath'},
 145                           $c->config->{'tempfiles_subdir'},
 146                           "cview",
 147                          );
 148 my ($fh ,$native_tmp) = tempfile( DIR => $native_format_tempdir, TEMPLATE=>"vector_XXXXXX");
 149
 150 foreach my $c (@$commands_ref) {
 151 print $fh join ", ", @$c;
 152 print $fh "\n";
 153 }
 154
 155 my $base_temp = basename ($native_tmp);
 156
 157
 158
 159
 160 ################################################################################
 161 display_results($p, $image_html, $seq, $commands_ref, $show_re, $base_temp);
 162 ###############################################################################
 163
 164 sub display_form {
 165     my $p = shift;
 166
 167 # display form
 168 #
 169 $p->header("Vector drawing application", "Vector drawing application");
 170
 171 print <<HTML;
 172
 173 <form enctype="multipart/form-data" method="post" >
 174 Vector name <input type="text" name="name" value="" size="8" /><br /><br />
 175 Upload a genbank file <input type="file" name="genbank_record" /><br /><br />
 176 <b>Format:</b><br />
 177 <input type="radio" name="format" value="genbank" checked="1" /> Genbank<br />
 178 <input type="radio" name="format" value="native" /> Native<br /><br />
 179 <b>Show restriction sites</b><br />
 180 <input type="radio" name="show_re" value="all" /> all (not recommended)<br />
 181 <input type="radio" name="show_re" value="unique" /> unique cutters<br />
 182 <input type="radio" name="show_re" value="popular6bp" /> popular 6bp cutters<br />
 183 <input type="radio" name="show_re" value="popular4bp" /> popular 4bp cutters<br />
 184 <br /><br />
 185 <input type="submit" value="upload" />
 186 <input type="hidden" name="action" value="upload" />
 187 </form>
 188
 189
 190 HTML
 191
 192 $p->footer();
 193
 194 }
 195
 196 sub display_results {
 197
 198     my $p = shift;
 199     my $image_html = shift;
 200     my $seq = shift;
 201     my $commands = shift;
 202     my $show_re = shift;
 203     my $native_file =shift;
 204     $p->header("Vector Drawing", "Vector Drawing");
 205
 206     print <<HTML;
 207
 208
 209 <center>
 210       $image_html
 211 </center>
 212
 213 HTML
 214
 215 my $html = qq{
 216
 217 <form method="post" >
 218 <input type="hidden" name="format" value="native" />
 219 <input type="hidden" name="action" value="draw_native" />
 220 <center>
 221 <textarea name="edit_commands" rows="20" cols="80">};
 222
 223     $native_commands = "";
 224     foreach my $c (@$commands) {
 225         $native_commands .= join ", ", @$c;
 226         $native_commands .= "\n";
 227     }
 228
 229     $html .= $native_commands;
 230     $html .=  qq { </textarea><br /><input type="submit" /></center></form> };
 231
 232     my $edit_native = info_section_html( title=> "Edit", contents=>$html, collapsible=>1, collapsed=>1);
 233
 234     print $edit_native;
 235
 236
 237     my $insert_html = <<HTML;
 238 <form method="post">
 239 Insert Sequence <br /><br /><textarea name="insert_sequence" value="" rows = "4" cols="80" /></textarea><br />
 240 Insert at position <input type="text" name="insert_coord" value="0" size="4" /><br />
 241 <input type="hidden" name="action" value="insert" />
 242
 243 <input type="hidden" name="native_file" value="$native_file" />
 244 <input type="hidden" name="show_re" value="$show_re" />
 245 <input type="submit" />
 246 </form>
 247
 248 HTML
 249
 250 print info_section_html( title=>"Insert sequence", contents=>$insert_html, collapsible=>1, collapsed=>1);
 251
 252     my $delete_html = <<HTML;
 253 <form method="post">
 254 Delete Sequence<br /><br />
 255 From position <input type="text" name="del_start" />
 256 to position <input type="text" name="del_end" />
 257 <input type="hidden" name="action" value="delete" />
 258 <input type="hidden" name="native_file" value="$native_file" />
 259 <input type="hidden" name="show_re" value="$show_re" />
 260 <input type="submit" />
 261 HTML
 262
 263 print info_section_html (title=>"Delete sequence", contents=>$delete_html, collapsible=>1, collapsed=>1);
 264
 265     my $split_seq = html_break_string($seq, 100, "\n");
 266     my $sequence_html = qq { <pre><div id="sequence_display">$split_seq</div></pre> };
 267
 268     print info_section_html( title=>"View sequence", contents=>$sequence_html, collapsible=>1, collapsed=>1);
 269
 270     $p->footer();
 271
 272
 273 }
 274