cgi-bin/tools/insilicopcr/index.pl

   1 =head1 NAME
   2
   3 index.pl - In Silico PCR web interface
   4
   5 =head1 DESCRIPTION
   6
   7 This interface shows a form that requires user input of the forward primer,
   8 reverse primer, maximum product size, Allowed mismathces. Also, In Silico
   9 PCR is dependent on the BLAST similarity search. Part of the blast code was
  10 used here to get the database, program, matrix, e-value.
  11 This page will forward the input to pcr_blast_result.pl and will then display
  12 the results in view_result.pl.
  13
  14
  15 =head1 DEPENDENCIES
  16
  17 Alot of the BLAST code in /sgn/cgi-bin/tool/blast was reused here
  18 PCR is dependent on the BLAST search to find the primers in the databases
  19
  20 =head1 AUTHOR
  21
  22 Waleed Haso wh292@cornell.edu
  23 Only added modifications to support the PCR part
  24 Original code was aspired from BLAST.
  25
  26 =cut
  27
  28
  29
  30 use strict;
  31 use warnings;
  32 use POSIX;
  33
  34 use CXGN::DB::Connection;
  35 use CXGN::Page;
  36 use CXGN::BlastDB;
  37 use CXGN::Page::FormattingHelpers qw/page_title_html info_table_html hierarchical_selectboxes_html /;
  38 use CXGN::Page::UserPrefs;
  39 use CXGN::Tools::List qw/evens distinct/;
  40
  41 my $page = CXGN::Page->new("In Silico PCR form","Waleed");
  42 my $dbh = CXGN::DB::Connection->new;
  43 our $prefs = CXGN::Page::UserPrefs->new( $dbh );
  44
  45 $page->header('In Silico PCR');
  46
  47 my ($databases,$programs,$programs_js) = blast_db_prog_selects();
  48
  49 ##############################################################################################################################
  50
  51 print page_title_html("In Silico PCR");
  52
  53
  54
  55   print <<EOF;
  56
  57 <HR></HR>
  58 <form method="post" action="pcr_blast_result.pl" name="PCRform" enctype="multipart/form-data">
  59    <input type="hidden" name="outformat" value="8" />
  60
  61   <table id="PCRinput" align="center" summary="" cellpadding="0" cellspacing="15" border="0">
  62         <tr>
  63         <td>
  64                 <H2><B> PCR Primers:</B></H2>
  65         </td>
  66     </tr>
  67         <tr>
  68                 <td>
  69                 <B> Forward Primer</B>
  70         </td>
  71         <td>
  72                 <input type="text" size="65" value="" name="fprimer" />
  73         </td>
  74     </tr>
  75         <tr>
  76                 <td>
  77                 <B>Reverse Complement Forward Primer</B>
  78         </td>
  79         <td>
  80                         <input type="checkbox" name="frevcom" />
  81         </td>
  82     </tr>
  83         <tr>
  84                 <td>
  85                 <B> Reverse Primer</B>
  86         </td>
  87         <td>
  88                 <input type="text" size="65" value="" name="rprimer" />
  89         </td>
  90     </tr>
  91         <tr>
  92                 <td>
  93                 <B>Reverse Complement Reverse Primer</B>
  94         </td>
  95         <td>
  96                         <input type="checkbox" name="rrevcom" />
  97         </td>
  98     </tr>
  99     <tr>
 100         <td>
 101                 <b>Product Maximum Length</b>
 102         </td>
 103         <td >
 104                 <input type="text" size="5" value="5000" name="productLength" />
 105         </td>
 106     </tr>
 107     <tr>
 108         <td>
 109                 <b>Allowed Mismatches</b>
 110         </td>
 111         <td >
 112                 <input type="text" size="5" value="0" name="allowedMismatches" />
 113         </td>
 114     </tr>
 115     <tr>
 116         <td>
 117                 <H2><B> BLAST Attributes:</B></H2>
 118         </td>
 119     </tr>
 120
 121     <tr>
 122         <td>
 123                 <b>Database (<tt>-d</tt>)</b>
 124         </td>
 125         <td>
 126                 $databases <a style="font-size: 80%" title="View details of each database" href="/tools/blast/dbinfo.pl">db details</a>
 127         </td>
 128     </tr>
 129     <tr>
 130         <td>
 131                 <b>BLAST Program (<tt>-p</tt>)</b>
 132         </td>
 133         <td>
 134                 $programs
 135         </td>
 136     </tr>
 137     <tr>
 138         <td>
 139                 <b>Substitution Matrix (<tt>-M</tt>)</b>
 140         </td>
 141         <td >
 142             <select name="matrix">
 143             <option value="BLOSUM62">BLOSUM62 (default)</option>
 144             <option value="BLOSUM80">BLOSUM80 (recent divergence)</option>
 145             <option value="BLOSUM45">BLOSUM45 (ancient divergence)</option>
 146             <option value="PAM30">PAM30</option>
 147             <option value="PAM70">PAM70</option>
 148             </select>
 149         </td>
 150     </tr>
 151     <tr>
 152         <td>
 153                 <b>Expectation value (<tt>-e</tt>)</b>
 154         </td>
 155         <td >
 156                 <input type="text" size="10" value="0.01" name="expect" />
 157         </td>
 158     </tr>
 159     <tr><td><b>Filter query sequence (DUST with blastn, SEG with others) (<tt>-F</tt>)</b></td>
 160         <td><input type="checkbox" checked="checked" name="filterq" /></td>
 161     </tr>
 162     <tr>
 163         <td align="right"><input type="reset" value="Clear" /></td>
 164         <td align="center"><input type="submit" name="search" value="  Run  " style="background: yellow; font-size: 130%" /></td>
 165     </tr>
 166   </table>
 167 </form>
 168 <script language="JavaScript" type="text/javascript">
 169 $programs_js
 170 </script>
 171 EOF
 172
 173 #}#end of the commented else
 174
 175 $page->footer();
 176
 177 ##########################################################################################################################
 178 #This subroutine is copied exactly from the BLAST index.pl code
 179
 180 sub blast_db_prog_selects {
 181   sub opt {
 182     my $db = shift;
 183     my $timestamp = $db->file_modtime
 184       or return '';
 185     $timestamp = strftime(' &nbsp;(%m-%d-%y)',gmtime $db->file_modtime);
 186     my $seq_count = $db->sequences_count;
 187
 188     [$db->blast_db_id, $db->title.$timestamp]
 189   }
 190
 191   my @db_choices = map {
 192     my @dbs = map [$_,opt($_)], grep $_->file_modtime, $_->blast_dbs( web_interface_visible => 't');
 193     @dbs ? ('__'.$_->name, @dbs) : ()
 194   } CXGN::BlastDB::Group->search_like(name => '%',{order_by => 'ordinal, name'});
 195
 196   my @ungrouped_dbs = grep $_->file_modtime,CXGN::BlastDB->search( blast_db_group_id => undef, web_interface_visible => 't', {order_by => 'title'} );
 197   if(@ungrouped_dbs) {
 198     push @db_choices, '__Other',  map [$_,opt($_)], @ungrouped_dbs;
 199   }
 200
 201   @db_choices or return '<span class="ghosted">The BLAST service is temporarily unavailable, we apologize for the inconvenience</span>';
 202
 203   my $selected_db_file_base = $prefs->get_pref('last_blast_db_file_base');
 204   #warn "got pref last_blast_db_file_base '$selected_db_file_base'\n";
 205
 206   my %prog_descs = ( blastn  => 'BLASTN (nucleotide to nucleotide)',
 207                      blastx  => 'BLASTX (nucleotide to protein; query translated to protein)',
 208                      blastp  => 'BLASTP (protein to protein)',
 209                      tblastx => 'TBLASTX (protein to protein; both database and query are translated)',
 210                      tblastn => 'TBLASTN (protein to nucleotide; database translated to protein)',
 211                    );
 212
 213   my @program_choices = map {
 214     my ($db) = @$_;
 215     if($db->type eq 'protein') {
 216       [map [$_,$prog_descs{$_}], 'blastx','blastp']
 217     } else {
 218       [map [$_,$prog_descs{$_}], 'blastn','tblastx','tblastn']
 219     }
 220   } grep ref, @db_choices;
 221
 222   @db_choices = map {ref($_) ? $_->[1] : $_} @db_choices;
 223
 224   return hierarchical_selectboxes_html( parentsel => { name => 'database',
 225                                                        choices =>
 226                                                        \@db_choices,
 227                                                        $selected_db_file_base ? (selected => $selected_db_file_base) : (),
 228                                                      },
 229                                         childsel  => { name => 'program',
 230                                                      },
 231                                         childchoices => \@program_choices
 232                                       );
 233 }