cgi-bin/tools/intron_detection/display_introns.pl

   1
   2 use strict;
   3 use warnings;
   4
   5 use IO::Scalar;
   6 use File::Temp;
   7 use File::Spec;
   8 use CXGN::Debug;
   9 use CXGN::BlastDB;
  10 use CXGN::Page;
  11 use CXGN::Page::FormattingHelpers qw/page_title_html/;
  12 use SGN::IntronFinder::Homology;
  13
  14 my $d = CXGN::Debug->new();
  15
  16 my $page = CXGN::Page->new( "Intron Finder Results", "Emil" );
  17
  18 my $temp_file_path = $page->path_to($page->tempfiles_subdir('intron_detection'));
  19
  20 $page->add_style( text => <<EOS );
  21 a[href^="http:"] {
  22   padding-right: 0;
  23   background: none;
  24 }
  25 EOS
  26
  27 my ( $input, $blast_e_val ) = $page->get_arguments( "genes", "blast_e_value" );
  28 $input =~ s/\r//g;    #remove weird line endings
  29 $input =~ s/^\s+|\s+$//g; #< trim whitespace
  30 $input = ">web_sequence\n$input" unless $input =~ /^>/;
  31
  32 $blast_e_val =~ s/(^\s*|\s*)//g;
  33 if ( $blast_e_val !~ m/^\d+(e-\d+)?$/ ) {
  34     show_error(
  35         $page,
  36         'e_bad'          => 1,
  37         'seq_bad'        => 0,
  38         'seq_notindb'    => 0,
  39         'unfound_seq_id' => ''
  40     );
  41     return 1;
  42 }
  43
  44 my $out_file = File::Temp->new(
  45     TEMPLATE => 'intron-finder-output-XXXXXX',
  46     DIR      => $temp_file_path,
  47 );
  48 $out_file->close;    #< can't use this filehandle
  49
  50 $page->header();
  51 print page_title_html("Intron Finder Results");
  52
  53 $d->d("Runninge the intron finder command...\n");
  54
  55 my ($protein_db) = CXGN::BlastDB->search( file_base => 'ath/ATH_pep' ) or die "could not find ath/ATH_pep BLAST database";
  56
  57 my $gene_feature_file =
  58   ( $page->get_conf('intron_finder_database')
  59       || die 'no conf var intron_finder_database defined!' )
  60   . "/SV_gene_feature.data";
  61
  62 -f $gene_feature_file or die "gene feature file '$gene_feature_file' not found";
  63
  64 print '<pre>';
  65 my $output;
  66 open my $input_fh, '<', \$input or die $!;
  67 open my $output_fh, '>', \$output or die $!;
  68
  69 SGN::IntronFinder::Homology::find_introns_txt
  70     ( $input_fh,
  71       $output_fh,
  72       $blast_e_val,
  73       $gene_feature_file,
  74       $temp_file_path,
  75       $protein_db->full_file_basename,
  76     );
  77 print $output;
  78 print '</pre>';
  79 print qq|<a href="find_introns.pl">Return to search page</a><br /><br />|;
  80
  81 $page->footer();
  82
  83 # show there was an error and link back to the entry page
  84 # possible arguments: e_bad => 0|1, seq_bad => 0|1, seq_notindb => 0|1,
  85 # unfound_seq_id => seq_id
  86 #
  87 sub show_error {
  88     my ( $page, %errors ) = @_;
  89
  90     $page->add_style( text => "p.error {font-weight: bold}" );
  91     $page->header();
  92     print page_title_html("Bad Input");
  93     if ( $errors{e_bad} ) {
  94         print
  95 "<p class=\"error\">E-value for blast should be an integer or in xe-xx format.</p>";
  96     }
  97     if ( $errors{seq_bad} ) {
  98         print "<p class=\"error\">Please enter your query in FASTA format.</p>";
  99     }
 100     elsif ( $errors{seq_notindb} ) {
 101         print
 102 "<p class=\"error\">EST identifier $errors{unfound_seq_id} could not be found in the database. Please enter a DNA sequence for it.</p>";
 103     }
 104
 105     print "<p><a href=\"find_introns.pl\">Go back</a> and try again.</p>";
 106     $page->footer();
 107 }