cgi-bin/sequencing/bac_registry_discrepancies.pl

   1 use strict;
   2 use warnings;
   3
   4 use Carp;
   5 use FindBin;
   6 use Getopt::Std;
   7
   8 use File::Find;
   9 use File::Basename;
  10
  11 use CXGN::DB::Connection;
  12
  13 use CXGN::Metadata;
  14 use CXGN::Genomic::CloneIdentifiers qw/parse_clone_ident/;
  15 use CXGN::Genomic::Clone;
  16 use CXGN::Genomic::Search::Clone;
  17 use CXGN::Tools::Identifiers qw/link_identifier/;
  18
  19 use CXGN::Page;
  20 use CXGN::Page::FormattingHelpers qw/columnar_table_html/;
  21 use CatalystX::GlobalContext qw( $c );
  22
  23 my $page = CXGN::Page->new('BAC Registry <-> FTP Discrepancies','Robert Buels');
  24
  25 $page->header('BAC Registry <-> FTP Discrepancies','BAC Registry <-> FTP Discrepancies');
  26
  27 my $ftp_path = $c->config->{'ftpsite_root'};
  28
  29 if(-d $ftp_path ) {
  30   my %sequenced_bacs = map {
  31     my ($bacname,$dirname) = fileparse($_,qr|\..+$|)
  32       or return;
  33     my $parsed = parse_clone_ident($bacname,'agi_bac_with_chrom')
  34       or return;
  35     #        $parsed->{match} eq $bacname
  36     #    or return;
  37     $parsed->{dirname} = $dirname;
  38
  39     #return
  40     ($bacname => $parsed)
  41   } glob(File::Spec->catfile($ftp_path,'tomato_genome','bacs','chr*','*finished','*.tar.gz'));
  42
  43   my @discrepancies;
  44   my @sequenced_bac_names = sort keys %sequenced_bacs;
  45
  46   foreach my $bacname (@sequenced_bac_names) {
  47     my $clone = CXGN::Genomic::Clone->retrieve_from_parsed_name($sequenced_bacs{$bacname})
  48       or die "Could not retrieve clone $bacname\n";
  49     $sequenced_bacs{$bacname}->{clone_object} = $clone;
  50     my $dirname = $sequenced_bacs{$bacname}->{dirname};
  51     my $truestatus = $dirname =~ m|unfinished| ? 'in_progress' : 'complete';
  52     my ($chr_from_dir) = $dirname =~ /chr(\d{2})/;
  53     $chr_from_dir += 0;         #make sure it's numeric
  54     $sequenced_bacs{$bacname}->{true_status} = $truestatus;
  55     unless( $clone->sequencing_status eq $truestatus ) {
  56       push @discrepancies,
  57         [
  58 #        $clone->clone_id,
  59           $clone->chromosome_num || $chr_from_dir,
  60           link_identifier($clone->clone_name_with_chromosome || $clone->clone_name,'bac'),
  61           $truestatus,
  62           $clone->sequencing_status,
  63 #         $dirname,
  64         ];
  65     }
  66     #   else {
  67     #     print "actually right!\n";
  68     #   }
  69   }
  70
  71   #now find all the BACs that are marked complete in the database and aren't
  72   #found on the filesystem
  73   my $search = CXGN::Genomic::Search::Clone->new;
  74   my $query = $search->new_query;
  75   $query->sequencing_status('=?','complete');
  76   my $results = $search->do_search($query);
  77   $results->autopage($query,$search);
  78   while (my $clone = $results->next_result) {
  79     my $chrname = $clone->clone_name_with_chromosome;
  80     #  print $clone->clone_name." = $chrname\n";
  81     unless ( my $record = $sequenced_bacs{$chrname} ) {
  82       push @discrepancies,
  83         [
  84 #        $clone->clone_id,
  85          $clone->chromosome_num || '',
  86          link_identifier($chrname,'bac'),
  87          'not present',
  88          $clone->sequencing_status,
  89 #        '',
  90         ];
  91     }
  92     #   else {
  93     #     print "actually right!\n"
  94     #   }
  95   }
  96
  97   print( '<center>',
  98          columnar_table_html( headings => ['Chr','Name','On FTP','In Database'],
  99                               data     => [sort {$a->[0] <=> $b->[0]
 100                                                  || $a->[1] cmp $b->[1]
 101                                                } @discrepancies
 102                                           ],
 103                               __tableattrs => 'width="50%" cellspacing="0"',
 104                             ),
 105          '</center>',
 106        );
 107 } else {
 108   print '<center>Sorry, this page is temporarily unavailable.</center>';
 109 }
 110
 111 $page->footer;