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

   1 use CatalystX::GlobalContext qw( $c );
   2 use strict;
   3 use warnings;
   4
   5 use CGI ();
   6 use Data::Dumper;
   7
   8 use CXGN::BioTools::AGP qw/ agp_contigs agp_contig_seq agp_parse /;
   9 use CXGN::TomatoGenome::BACPublish qw/ agp_file /;
  10 use CXGN::Publish;
  11
  12 my $cgi = CGI->new;
  13 my $publisher = CXGN::Publish->new;
  14 my $bcs = $c->dbic_schema('Bio::Chado::Schema');
  15
  16 if( my $contig_name = $cgi->param('contig') ) {
  17     $contig_name =~ s/[^\w\.]//g; #< sanitize the contig name
  18
  19     my $p = CXGN::Tools::Identifiers::parse_identifier($contig_name,'tomato_bac_contig')
  20         or $c->throw( message => "Invalid contig identifier $contig_name", is_error => 0 );
  21
  22     my $agp_file_unversioned = agp_file( $p->{chr}, 'unpublished' )
  23         or $c->throw( message => 'No AGP file found for chromosome '.$p->{chr} );
  24
  25     my $agp_publishing_record = $publisher->publishing_history( $agp_file_unversioned );
  26     #$c->throw( message => 'break', developer_message => '<pre>'.Dumper($agp_publishing_record).'</pre>' );
  27
  28     # hash of file version => publishing record (which is { version => $num, fullpath => path to file })
  29     my %agp_versions = map { $_->{version} => $_ }
  30         ( $agp_publishing_record, @{ $agp_publishing_record->{ancestors} || []} );
  31
  32     my $agp_file = $agp_versions{ $p->{ver} }->{fullpath}
  33         or $c->throw( message => "No AGP file found for chromosome $p->{chr} version $p->{ver}",
  34                       developer_message => join '', (
  35                           "<pre>",
  36                           Dumper({ agp_versions => \%agp_versions,
  37                                    agp_publishing_record => $agp_publishing_record,
  38                                    agp_file_unversioned => $agp_file_unversioned
  39                                   }),
  40                           '</pre>',
  41                          ),
  42                      );
  43
  44     my @contigs = agp_contigs( agp_parse( $agp_file ) );
  45     my $contig = $contigs[ $p->{ctg_num} - 1 ]
  46         or $c->throw( message => "No contig $p->{ctg_num} found in AGP for chromosome $p->{chr}.$p->{ver}",
  47                       developer_message => join '', (
  48                           "<pre>",
  49                           Dumper({ contigs => \@contigs,
  50                                    contig_count => scalar(@contigs),
  51                                    agp_file => $agp_file,
  52                                 }),
  53                           '</pre>',
  54                          ),
  55                      );
  56
  57     $c->forward_to_mason_view(
  58         '/genomes/Solanum_lycopersicum/sequencing/view_contig/view.mas',
  59         contig      => $contig,
  60         contig_name => $contig_name,
  61         seq_source => sub {
  62             my $seq_name = shift;
  63             my $feat = $bcs->resultset('Sequence::Feature')->search({name => $seq_name},{rows => 1})->single
  64                 or $c->throw( message => "Sequence $seq_name not found" );
  65             #die Dumper({ name => $feat->id, residues => $feat->seq });
  66             return $feat->residues; #< feature acts as a Bio::PrimarySeqI
  67         },
  68        );
  69 } else {
  70     $c->forward_to_mason_view('/genomes/Solanum_lycopersicum/sequencing/view_contig/input.mas');
  71 }