cgi-bin/sequencing/tpf.pl

   1
   2 use strict;
   3
   4 use File::Temp qw//;
   5 use File::Spec;
   6
   7 use CXGN::DB::Connection;
   8 use CXGN::TomatoGenome::BACPublish qw/tpf_agp_files/;
   9 use CXGN::Genomic::Clone;
  10 use CXGN::Genomic::CloneIdentifiers qw/parse_clone_ident/;
  11 use CXGN::Login;
  12 use CXGN::Page;
  13 use CXGN::Page::FormattingHelpers qw( info_section_html
  14                                       page_title_html
  15                                       columnar_table_html
  16                                       info_table_html
  17                                       modesel
  18                                     );
  19 use CXGN::People;
  20 use CXGN::Publish qw/publish/;
  21
  22 #tpf_agp is in the current directory
  23 use CXGN::TomatoGenome::tpf_agp qw(
  24                                    format_validation_report
  25                                    filename
  26                                    published_ftp_download_links
  27                                    tabdelim_to_html
  28                                    tabdelim_to_array
  29                                    modtime_string
  30                                   );
  31
  32 my $page = CXGN::Page->new("Tiling Path Display","Rob");
  33 my $dbh = CXGN::DB::Connection->new();
  34
  35 #get input arguments and validate
  36 my ($chr) = $page->get_arguments(qw/chr/);
  37 $chr += 0; #force chr to be numeric
  38 $chr ||= 1;
  39
  40 #if we have a file upload, validate it according to its type and store it
  41 if(my $upload = $page->get_upload ) {
  42   #get the active login
  43   my $sp_person_id = CXGN::Login->new($dbh)->verify_session();
  44   my $sp = CXGN::People::Person->new($dbh, $sp_person_id);
  45   $sp->get_username
  46     or do {print $page->header; graceful_exit("Username not found.")};
  47
  48   #check that the login has permission to upload for this chromosome
  49   unless($sp->get_user_type eq 'curator'
  50          || grep {$_ == $chr && $_ <= 12 && $_ >= 1} $sp->get_projects_associated_with_person) {
  51     print $page->header(); graceful_exit('your account does not have privileges to upload files for that chromosome');
  52   }
  53
  54   my $validation_report = validate_and_publish_tpf($upload->fh,$chr);
  55   $page->message_page('TPF validation failed',$validation_report) if $validation_report;
  56 }
  57
  58
  59 $page->header('TPF Display',"Chromosome Tiling Paths");
  60 print <<EOHTML;
  61 <p>The tiling path listings below have been developed and submitted to
  62 SGN by the individual <a href="/about/tomato_sequencing.pl">tomato
  63 chromosome sequencing projects</a>.</p>
  64
  65 <p>The listing below shows the clones that make up the current planned
  66 tiling path for this chromosome, along with any gaps that have yet
  67 to be bridged by a sequence of clones.</p>
  68
  69 <p>It is in TPF format, which consists of three columns:</p>
  70 <ol>
  71   <li>the NCBI/EMBL Accession of the BAC sequence</li>
  72   <li>the SGN name of the BAC sequence</li>
  73   <li>a name for each contiguous group of BACs, internal to each chromosome sequencing project</li>
  74 </ol>
  75
  76 <p>These files are also available for download <a href="ftp://ftp.sgn.cornell.edu/tomato_genome/tpf">via FTP</a>.</p>
  77 EOHTML
  78
  79 if ($chr > 12 or $chr < 1){
  80   graceful_exit("Oops! Chromosome number must be between 1-12.");
  81 }
  82
  83 print qq|<div style="text-align: center; font-weight: bold; margin-bottom: 0.5em">Chromosome</div>\n|;
  84 print modesel( [map {["?chr=$_",$_]} 1..12], $chr-1);
  85 print "<br />\n";
  86
  87
  88 #now show the current tpf and agp files
  89
  90 my $published_tpf;
  91 eval {
  92   ($published_tpf,undef) = tpf_agp_files($chr);
  93 };
  94 if ($@){
  95   graceful_exit($@);
  96 }
  97
  98 my ($published_tpf_ftp,undef) = published_ftp_download_links($chr);
  99 print info_section_html( title    => 'Tiling Path Format (TPF)',
 100                          subtitle => modtime_string($published_tpf).'  '.$published_tpf_ftp,
 101                          contents => tpf_to_html($published_tpf) || <<EOHTML,
 102 <center><b>No TPF file is currently available for chromosome $chr</b></center>
 103 EOHTML
 104                        );
 105 print info_section_html( title    => "Other Chromosome $chr Resources",
 106                          contents =>  <<EOHTML,
 107 <ul>
 108 <li>Tomato maps: <a href="/cview/index.pl">Genetic</a> | <a href="/cview/map.pl?map_id=9&amp;physical=1">Physical</a> | <a href="/cview/map.pl?map_id=13">BAC FISH results</a></li>
 109 <li><a href="/tomato/genome_data.pl?chr=$chr">Chromosome $chr BACs in Genome Browser</a></li>
 110 <li><a href="agp.pl?chr=$chr">Chromosome $chr Assembly (AGP)</a></li>
 111 </ul>
 112 EOHTML
 113                        );
 114 $page->footer;
 115
 116
 117
 118 # we should NOT be using error_page! Use this instead!
 119 sub graceful_exit {
 120
 121   my ($message) = @_;
 122   print $message;
 123   print $page->footer;
 124   exit;
 125
 126 }
 127
 128 #CHECK:
 129 #correct number of columns
 130 #correct data type of each column
 131 #correctly formed bac identifiers
 132 #bac identifiers are on the correct chromosome
 133 sub validate_and_publish_tpf {
 134   my ($tpf_fh,$chr) = @_;
 135   my $publishing_filename = filename($chr,'tpf');
 136   my $tmp = File::Temp->new( UNLINK => 1, SUFFIX => '.tpf' );
 137   my @errors;
 138   my $line_ctr = 0;
 139   my $err = sub {
 140     push @errors, "Line $line_ctr: ".shift;
 141   };
 142   #copy the tpf file from the apache-spooled temp file.  while doing
 143   #that, go over each line and validate it
 144   while(my $line = <$tpf_fh>) {
 145     $line_ctr++;
 146     chomp $line;
 147     $line =~ s/\r$//;
 148     unless($line =~ /^\s*#/) {
 149       my @d = split /\s+/,$line;
 150       @d == 3 or $err->("Incorrect column count:  ".scalar(@d)." columns found");
 151       if( $d[0] =~ /^GAP$/ ) {
 152         $d[1] =~ /^type-[1234]$|/ or $err->("If first column is GAP, second column must be a type-[1234] gap type");
 153         $d[2] eq '?' or $err->("If first column is 'GAP', third column must be '?' (it is '$d[2]')");
 154       }
 155       elsif( $d[0] eq '?' || $d[0] =~ /^\S{5,}$/ ) {
 156         my $p = parse_clone_ident($d[1],qw/agi_bac_with_chrom agi_bac/)
 157             or $err->("If line is not a gap, second column must be a valid SGN BAC clone identifier");
 158         if($p) {
 159           my $c = CXGN::Genomic::Clone->retrieve_from_parsed_name($p)
 160             or $err->("Unknown clone identifier '$d[1]' in second column");
 161           if($c) {
 162             $c->chromosome_num == $chr
 163               or $err->("BAC with identifier '$d[1]' is not registered as being on chromosome $chr");
 164             $d[1] = $c->clone_name_with_chromosome;
 165           }
 166         }
 167       }
 168       else {
 169         $err->("Invalid first column '$d[0]'");
 170       }
 171       print $tmp join("\t",@d)."\n";
 172     } else {
 173       print $tmp "$line\n";
 174     }
 175   }
 176   close $tmp; #make sure we flush the writes we made
 177   if(@errors) {
 178     return format_validation_report(@errors);
 179   } else {
 180     publish(['cp', "$tmp", $publishing_filename]);
 181     return;
 182   }
 183 }
 184
 185 sub tpf_to_html {
 186   my ($filename) = @_;
 187   if($filename && -f $filename) {
 188     return tabdelim_to_html($filename,undef,
 189                         #this sub looks at the contents of each
 190                         #table cell and might emit some style rules
 191                         #to highlight it
 192                             sub {
 193                               my ($contents) = @_;
 194                               if ($contents =~ /^\s*#/) {
 195                                 'color: green'
 196                               } elsif ( $contents =~ /^\s*GAP\s*$/ ) {
 197                                 'color: red'
 198                               } elsif ( $contents =~ /^\s*\?\s*$/ ) {
 199                                 'font-weight: bold'
 200                               }
 201                             }
 202                            );
 203
 204   }
 205 }
 206