cgi-bin/maps/physical/clone_sequence.pl

   1 use strict;
   2 use CXGN::Genomic::Clone;
   3 use CXGN::Tools::Text;
   4 use CXGN::Page;
   5 use CXGN::Page::FormattingHelpers qw/page_title_html html_break_string/;
   6 use CXGN::Genomic::Tools qw/clone_annotation_sequence/;
   7
   8 my $page = CXGN::Page->new( 'Clone Sequence', 'john' );
   9 my ($clone_id) = $page->get_encoded_arguments('clone_id');
  10 my $clone = CXGN::Genomic::Clone->retrieve($clone_id)
  11   or do{ $page->error_page("No clone found with ID '$clone_id'"); exit };
  12
  13 my @seqnames  = $clone->latest_sequence_name;
  14 my @sequences = $clone->seq
  15   or $page->message_page( "No sequence information for clone "
  16       . $clone->clone_name
  17       . ".  If you think you reached this page in error, the database may be in the middle of an update.  Please try again later."
  18   );
  19 @seqnames == @sequences
  20   or die 'differing number of seqnames and seqs: '
  21   . scalar(@seqnames)
  22   . ' names vs '
  23   . scalar(@sequences) . ' seqs';
  24
  25 $page->header;
  26 print page_title_html( 'BAC Sequence &ndash; ' . $clone->clone_name );
  27
  28 foreach my $name (@seqnames) {
  29     my $sequence = shift @sequences;
  30     print(
  31         "<span class=\"sequence\">&gt;",
  32         $name, "<br />",
  33         html_break_string( $sequence, 100 ),
  34         "</span><br />",
  35     );
  36 }
  37 $page->footer;