cgi-bin/tools/blast/show_match_seq.pl

   1 use CatalystX::GlobalContext qw( $c );
   2
   3 =head1 NAME
   4
   5 NOTE: This script has been deprecated. The functionality was moved
   6 to SGN::Controller::Blast.
   7
   8 show_match_seq.pl - a simple script to show the entire sequence of a
   9 match in a blast database with optional highlighting of the matched
  10 region
  11
  12 =head1 DESCRIPTION
  13
  14 This script shows a webpage with the sequence from a blast database
  15 for a specific id, using CXGN::BlastDB. This is the script that should
  16 be called if the CXGN::Tools::Identifiers cannot determine an
  17 appropriate link, so that the users still can get at the matched
  18 sequence, instead of uselessly defaulting to Genbank.
  19
  20 Page arguments:
  21
  22 =over 10
  23
  24 =item id
  25
  26 The id of the sequence [string], as it appears in the database (best
  27 retrieved from a blast report).
  28
  29 =item blast_db_id
  30
  31 The id [int] of the blast database file for CXGN::BlastDB.
  32
  33 =item hilite_coords
  34
  35 a list of start and end coordinates, of the form:
  36
  37 start1-end1,start2-end2,start3-end3
  38
  39 =item format
  40
  41 either "text" or "html" to output fasta text or a nicely ;-) formatted
  42 html page.
  43
  44 =back
  45
  46 =head1 AUTHOR
  47
  48 Lukas Mueller <lam87@cornell.edu>
  49
  50 Robert Buels <rmb32@cornelle.edu>
  51
  52 =cut
  53
  54 use strict;
  55 use warnings;
  56
  57 use CGI ();
  58
  59 use CXGN::BlastDB;
  60 use CXGN::Tools::Text qw/ sanitize_string /;
  61 use CXGN::MasonFactory;
  62
  63 use CXGN::Page::FormattingHelpers qw | info_section_html html_break_string html_string_linebreak_and_highlight | ;
  64
  65 my $cgi = CGI->new;
  66
  67 #get params
  68 my ( $id            ) = $cgi->param( 'id'            );
  69 my ( $blast_db_id   ) = $cgi->param( 'blast_db_id'   );
  70 my ( $format        ) = $cgi->param( 'format'        );
  71 my ( $hilite_coords ) = $cgi->param( 'hilite_coords' );
  72
  73 #sanitize params
  74 $format      ||= 'html';
  75 $blast_db_id +=  0;
  76 $id          =   sanitize_string( $id );
  77
  78 $c->forward_to_mason_view('/blast/show_seq/input.mas') unless $blast_db_id && defined $id;
  79
  80 # parse the coords param
  81 my @coords =
  82     map {
  83         my ($s, $e) = split "-", $_;
  84         defined $_ or die 'parse error' for $s, $e;
  85         [ $s, $e ]
  86     }
  87     grep length,
  88     split ',',
  89     ( $hilite_coords || '' );
  90
  91 #die("hilite_coords $hilite_coords. ".(join ",", @coords)."\n");
  92
  93 # look up our blastdb
  94 my $bdbo = CXGN::BlastDB->from_id( $blast_db_id )
  95     or $c->throw( is_error => 0,
  96                   message => "The blast database with id $blast_db_id could not be found (please set the blast_db_id parameter).");
  97
  98 my $seq = $bdbo->get_sequence( $id ) # returns a Bio::Seq object.
  99     or $c->throw( is_error => 0,
 100                   message => "The sequence could not be found in the blast database with id $blast_db_id.");
 101
 102 # dispatch to the proper view
 103 if ( $format eq 'html' ) {
 104     my $view_link     = do { $cgi->param( format => 'fasta_text'); '?'.$cgi->query_string };
 105     my $download_link = do { $cgi->param( format => 'fasta_file'); '?'.$cgi->query_string };
 106
 107     $c->forward_to_mason_view(
 108         '/blast/show_seq/html.mas',
 109         seq              => $seq,
 110         highlight_coords => \@coords,
 111         source           => '"'.$bdbo->title.'" BLAST dataset ',
 112         format_links     => [
 113             ( $seq->length > 500_000 ? () : [ 'View as FASTA' => $view_link ] ),
 114             [ 'Download as FASTA' => $download_link ],
 115            ],
 116         blast_url => '/tools/blast/index.pl',
 117        );
 118
 119 } elsif( $format eq 'fasta_file' || $format eq 'fasta_text' ) {
 120
 121     require Bio::SeqIO;
 122
 123     print "Content-Type: text/plain\n";
 124     my $attachment = $format eq 'fasta_file' ? 'attachment;' : '';
 125     print "Content-Disposition: $attachment filename=$id.fa\n";
 126     print "\n";
 127     Bio::SeqIO->new( -fh => \*STDOUT, -format => 'fasta' )
 128               ->write_seq( $seq )
 129 }
 130
 131