cgi-bin/genomes/Solanum_lycopersicum/sequencing/view_bac_contig.pl

   1 use strict;
   2 use warnings;
   3
   4 use CGI ();
   5 use Data::Dumper;
   6
   7 use CXGN::BioTools::AGP qw/ agp_contigs agp_contig_seq agp_parse /;
   8 use CXGN::TomatoGenome::BACPublish qw/ agp_file /;
   9 use CXGN::Publish;
  10
  11 my $cgi = CGI->new;
  12 my $publisher = CXGN::Publish->new;
  13 my $bcs = $c->dbic_schema('Bio::Chado::Schema');
  14
  15 if( my $contig_name = $cgi->param('contig') ) {
  16     $contig_name =~ s/[^\w\.]//g; #< sanitize the contig name
  17
  18     my $p = CXGN::Tools::Identifiers::parse_identifier($contig_name,'tomato_bac_contig')
  19         or $c->throw( message => "Invalid contig identifier $contig_name", is_error => 0 );
  20
  21     my $agp_file_unversioned = agp_file( $p->{chr}, 'unpublished' )
  22         or $c->throw( message => 'No AGP file found for chromosome '.$p->{chr} );
  23
  24     my $agp_publishing_record = $publisher->publishing_history( $agp_file_unversioned );
  25     #$c->throw( message => 'break', developer_message => '<pre>'.Dumper($agp_publishing_record).'</pre>' );
  26
  27     # hash of file version => publishing record (which is { version => $num, fullpath => path to file })
  28     my %agp_versions = map { $_->{version} => $_ }
  29         ( $agp_publishing_record, @{ $agp_publishing_record->{ancestors} || []} );
  30
  31     my $agp_file = $agp_versions{ $p->{ver} }->{fullpath}
  32         or $c->throw( message => "No AGP file found for chromosome $p->{chr} version $p->{ver}",
  33                       developer_message => join '', (
  34                           "<pre>",
  35                           Dumper({ agp_versions => \%agp_versions,
  36                                    agp_publishing_record => $agp_publishing_record,
  37                                    agp_file_unversioned => $agp_file_unversioned
  38                                   }),
  39                           '</pre>',
  40                          ),
  41                      );
  42
  43     my @contigs = agp_contigs( agp_parse( $agp_file ) );
  44     my $contig = $contigs[ $p->{ctg_num} - 1 ]
  45         or $c->throw( message => "No contig $p->{ctg_num} found in AGP for chromosome $p->{chr}.$p->{ver}",
  46                       developer_message => join '', (
  47                           "<pre>",
  48                           Dumper({ contigs => \@contigs,
  49                                    contig_count => scalar(@contigs),
  50                                    agp_file => $agp_file,
  51                                 }),
  52                           '</pre>',
  53                          ),
  54                      );
  55
  56     $c->forward_to_mason_view(
  57         '/genomes/Solanum_lycopersicum/sequencing/view_contig/view.mas',
  58         contig      => $contig,
  59         contig_name => $contig_name,
  60         seq_source => sub {
  61             my $seq_name = shift;
  62             my $feat = $bcs->resultset('Sequence::Feature')->search({name => $seq_name},{rows => 1})->single
  63                 or $c->throw( message => "Sequence $seq_name not found" );
  64             #die Dumper({ name => $feat->id, residues => $feat->seq });
  65             return $feat->residues; #< feature acts as a Bio::PrimarySeqI
  66         },
  67        );
  68 } else {
  69     $c->forward_to_mason_view('/genomes/Solanum_lycopersicum/sequencing/view_contig/input.mas');
  70 }