[Bio] / Sprout / GenomeStats.pl Repository:
ViewVC logotype

Diff of /Sprout/GenomeStats.pl

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.30, Thu Dec 6 14:58:03 2007 UTC revision 1.32, Sun Mar 23 16:10:47 2008 UTC
# Line 2  Line 2 
2    
3  =head1 Genome Data Generator  =head1 Genome Data Generator
4    
5  This script creates a set of HTML include files that list the statistics for  This script creates a set of Wiki pages that list the statistics for
6  the genomes in each of the genome groups. Genomes that are new to this version  the genomes in each of the genome groups. Genomes that are new to this version
7  of the Sprout will be specially marked. In order for this to work, both the  of the Sprout will be specially marked. In order for this to work, both the
8  current and previous Sprout databases must be available on this machine.  current and previous Sprout databases must be available on this machine.
# Line 37  Line 37 
37    
38  Display this command's parameters and options.  Display this command's parameters and options.
39    
40  =item strict  =item test
41    
42  If specified, strict groups will be used; otherwise, groups with a common primary name  If specified, the output pages will be put into the sandbox instead of the main web.
 will be combined into a single group. (The primary name of the group is the first  
 capitalized word.)  
   
 =item oddStyle  
   
 Style to use for odd rows of the table.  
   
 =item evenStyle  
   
 Style to use for even rows of the table.  
   
 =item tableStyle  
   
 Style to use for the table itself.  
   
 =item markerStyle  
   
 Style to use for small-text markers (e.g. NEW!)  
   
 =item numStyle  
   
 Style to use for numeric cells.  
   
 =item counterStyle  
   
 Style to use for counter cells.  
   
 =item linkCGI  
   
 Path to the CGI script for displaying detailed statistics.  
43    
44  =item noNewCheck  =item noNewCheck
45    
# Line 84  Line 54 
54    
55  use strict;  use strict;
56  use Tracer;  use Tracer;
 use DocUtils;  
 use TestUtils;  
57  use Cwd;  use Cwd;
58  use File::Copy;  use File::Copy;
59  use File::Path;  use File::Path;
# Line 93  Line 61 
61  use SFXlate;  use SFXlate;
62  use CGI qw(:standard);  use CGI qw(:standard);
63  use FIG;  use FIG;
64    use WikiTools;
65    
66  # Get the command-line options and parameters.  # Get the command-line options and parameters.
67  my ($options, @parameters) = StandardSetup([qw(Sprout ERDB) ],  my ($options, @parameters) = StandardSetup([qw(Sprout ERDB) ],
68                                             {                                             {
69                                              strict => [0, 'keep related groups separate'],                                              test => [0, 'if specified, publishes to the wiki sandbox instead of the main web'],
                                             oddStyle => ['odd', 'style for odd rows'],  
                                             trace => [2, 'tracing level'],  
                                             evenStyle => ['even', 'style for even rows'],  
                                             tableStyle => ['genomestats', 'style for whole table'],  
                                             markerStyle => ['tinytext', 'style for markers'],  
                                             numStyle => ['numcell', 'style for cells with numeric values'],  
                                             counterStyle => ['countercell', 'style for cells with counter values'],  
                                             linkCGI => ['../FIG/genome_statistics.cgi',  
                                                         'path to CGI script for detailed statistics'],  
70                                              noNewCheck => [0, 'if specified, skips the check for new genomes'],                                              noNewCheck => [0, 'if specified, skips the check for new genomes'],
                                             targetDir => ["$FIG_Config::nmpdr_base/next/html/includes",  
                                                           'target directory'],  
71                                              },                                              },
72                                             "",                                             "",
73                                             @ARGV);                                             @ARGV);
# Line 121  Line 79 
79      # displayed along with the attribute values.      # displayed along with the attribute values.
80      my %specialCols = (Serotype => 'Serotype_code',      my %specialCols = (Serotype => 'Serotype_code',
81                         Phenotype => 'Phenotype');                         Phenotype => 'Phenotype');
82      # Verify the directory name.      my $outputWeb = ($options->{test} ? 'Sandbox' : 'Main');
     my $targetDir = $options->{targetDir};  
     if (! $targetDir) {  
         Confess("No target directory specified.");  
     } elsif (! -d $targetDir) {  
         Confess("Target directory $targetDir not found.");  
     } else {  
83          # Get the new Sprout.          # Get the new Sprout.
84          my $sprout = SFXlate->new_sprout_only();          my $sprout = SFXlate->new_sprout_only();
85          my %newGroupHash = $sprout->GetGroups();          my %newGroupHash = $sprout->GetGroups();
86        # Get a wiki helper.
87        my $wiki = WikiTools->new();
88          # Extract the genome group data from the new Sprout.          # Extract the genome group data from the new Sprout.
         if (! $options->{strict}) {  
89              %newGroupHash = $sprout->Fix(%newGroupHash);              %newGroupHash = $sprout->Fix(%newGroupHash);
         }  
90          # This hash will be used to determine which genomes are new.          # This hash will be used to determine which genomes are new.
91          my %oldGroupHash = ();          my %oldGroupHash = ();
92          if ($options->{noNewCheck}) {          if ($options->{noNewCheck}) {
# Line 146  Line 98 
98              my $oldSprout = SFXlate->old_sprout_only();              my $oldSprout = SFXlate->old_sprout_only();
99              # Extract the genome group data from the old Sprout.              # Extract the genome group data from the old Sprout.
100              %oldGroupHash = $oldSprout->GetGroups();              %oldGroupHash = $oldSprout->GetGroups();
             if (! $options->{strict}) {  
101                  %oldGroupHash = $oldSprout->Fix(%oldGroupHash);                  %oldGroupHash = $oldSprout->Fix(%oldGroupHash);
102              }              }
         }  
103          # Get a FIG object for computing attributes.          # Get a FIG object for computing attributes.
104          my $fig = FIG->new();          my $fig = FIG->new();
105          # Get the super-group list.          # Get the super-group list.
# Line 158  Line 108 
108          my %linkParms = ( s0 => "nothypo_sub", n0 => "nothypo_nosub",          my %linkParms = ( s0 => "nothypo_sub", n0 => "nothypo_nosub",
109                            s1 => "hypo_sub", n1 => "hypo_nosub" );                            s1 => "hypo_sub", n1 => "hypo_nosub" );
110          my @columnTypes = ('s0', 'n0', 's1', 'n1');          my @columnTypes = ('s0', 'n0', 's1', 'n1');
         # Get the styles.  
         my ($tableStyle, $markerStyle, @rowStyle) = ($options->{tableStyle}, $options->{markerStyle},  
                                                      $options->{evenStyle}, $options->{oddStyle});  
         my ($numStyle, $counterStyle) = ($options->{numStyle}, $options->{counterStyle});  
111          # Prepare a hash for the summary counters. These will be used on the organism summary page.          # Prepare a hash for the summary counters. These will be used on the organism summary page.
112          my %summaries = ();          my %summaries = ();
113          # Loop through the groups.          # Loop through the groups.
# Line 178  Line 124 
124              if (exists $oldGroupHash{$groupID}) {              if (exists $oldGroupHash{$groupID}) {
125                  %oldGenomes = map { $_ => 1 } @{$oldGroupHash{$groupID}};                  %oldGenomes = map { $_ => 1 } @{$oldGroupHash{$groupID}};
126              }              }
127              # Create the output file.          # Compute the name of the wiki page we're building.
128              my $outFileName = "stats-" . lc($groupID) . ".inc";          my $outPageName = "${groupID}Stats";
129              Open(\*GROUPFILE, ">$targetDir/$outFileName");          # We'll put the data for the page in here.
130            my @outputLines = ();
131              # Get the special columns. We'll stuff them in a hash keyed by column name. Each column name will contain              # Get the special columns. We'll stuff them in a hash keyed by column name. Each column name will contain
132              # a sub-hash that translates each genome ID to its applicable attribute value (if any).              # a sub-hash that translates each genome ID to its applicable attribute value (if any).
133              my %specialData = ();              my %specialData = ();
# Line 193  Line 140 
140                      $specialData{$specialColumn} = \%specialDataList;                      $specialData{$specialColumn} = \%specialDataList;
141                  }                  }
142              }              }
143              # Set up the column names.          # Set up the column names. Note that an extra space in front of a name will be interpreted by
144              my @columnNames = "Strain annotated in NMPDR";          # the Wiki markup as an order to right-justify the text.
145              push @columnNames, sort keys %specialData;          my @columnNames = "*Strain annotated in NMPDR*";
146              push @columnNames,  "Genome size, bp",          push @columnNames, map { "*$_*" } sort keys %specialData;
147                                  "Protein Encoding Genes (PEGs)",          push @columnNames,  "*Genome size, bp*",
148                                  "Named genes in subsystems",            # s0                              " *[[FIG.ProteinEncodingGenes][Protein Encoding Genes]] (PEGs)*",
149                                  "Named genes not in subsystems",        # n0                              " *Named genes in subsystems*",            # s0
150                                  "Hypothetical genes in subsystems",     # s1                              " *Named genes not in subsystems*",        # n0
151                                  "Hypothetical genes not in subsystems", # n1                              " *Hypothetical genes in subsystems*",     # s1
152                                  "Subsystems",                              " *Hypothetical genes not in subsystems*", # n1
153                                  "RNAs";                              " *Subsystems*",
154              # Start the table.                              " *RNAs*";
             print GROUPFILE "<table class=\"$tableStyle\">\n";  
155              # Create the header row.              # Create the header row.
156              print GROUPFILE Tr( { class => 'odd' }, th(\@columnNames)) . "\n";          push @outputLines, "| " . join(" | ", @columnNames) . " |";
157              # The data rows will be built next. We'll be putting them into a hash keyed by              # The data rows will be built next. We'll be putting them into a hash keyed by
158              # organism name. The hash enables us to spit them out sorted by name.              # organism name. The hash enables us to spit them out sorted by name.
159              my %rows = ();              my %rows = ();
# Line 223  Line 169 
169                  # Get the strain name.                  # Get the strain name.
170                  my $genomeName = $sprout->GenusSpecies($genomeID);                  my $genomeName = $sprout->GenusSpecies($genomeID);
171                  # Apply a link.                  # Apply a link.
172                  my $genomeText = CGI::a({ href => "../FIG/genome_statistics.cgi?genome=$genomeID;SPROUT=1" }, $genomeName);              my $genomeText = "%SV{\"$genomeName\" id=\"$genomeID\"}%";
173                  # If this is a new strain, build the HTML for the NEW! mark.              # If this is a new strain, add the NEW! mark.
174                  if ($new) {                  if ($new) {
175                      $new = " <span class=\"$markerStyle\">NEW!</span>";                  $genomeText .= " %N%";
176                  }                  }
177                  # Get the genome length.                  # Get the genome length.
178                  $num = $sprout->GenomeLength($genomeID);                  $num = $sprout->GenomeLength($genomeID);
# Line 273  Line 219 
219                  $groupTotals{features} += $totalFeatures;                  $groupTotals{features} += $totalFeatures;
220                  # We have all our data. Next we need to compute the percentages and the links.                  # We have all our data. Next we need to compute the percentages and the links.
221                  # First, the link stuff.                  # First, the link stuff.
222                  my $linkPrefix = "$options->{linkCGI}?user=\&genome=$genomeID&SPROUT=1&request=";              my $linkPrefix = "%NMPDR{FIG/genome_statistics.cgi}%?user=;genome=$genomeID;SPROUT=1;request=";
223                  # Now format the counters and percentages.                  # Now format the counters and percentages.
224                  for my $type (keys %linkParms) {                  for my $type (keys %linkParms) {
225                      $counters{$type} = a( { href => "$linkPrefix$linkParms{$type}" },                      $counters{$type} = a( { href => "$linkPrefix$linkParms{$type}" },
# Line 287  Line 233 
233                  my $ssLink = "$options->{linkCGI}?user=\&genome=$genomeID&SPROUT=1&show_subsystems=1";                  my $ssLink = "$options->{linkCGI}?user=\&genome=$genomeID&SPROUT=1&show_subsystems=1";
234                  my $ssCol = "<a href=\"$ssLink\">$ssCount</a>";                  my $ssCol = "<a href=\"$ssLink\">$ssCount</a>";
235                  # Start creating the table cells.                  # Start creating the table cells.
236                  my $rowHtml = td("$genomeText$new");              my $rowHtml = "| $genomeText |";
237                  # Add any special columns.                  # Add any special columns.
238                  for my $specialCol (keys %specialData) {                  for my $specialCol (keys %specialData) {
239                      # Here we get the attribute value. If there is none, we leave the column blank.                      # Here we get the attribute value. If there is none, we leave the column blank.
240                      my $attribute = $specialData{$specialCol}->{$genomeID} || "&nbsp;";                      my $attribute = $specialData{$specialCol}->{$genomeID} || "&nbsp;";
241                      $rowHtml .= td($attribute);                  $rowHtml .= " $attribute |";
242                  }                  }
243                  # Now add the data columns.                  # Now add the data columns.
244                  $rowHtml .= join("",              $rowHtml .= join("", map { "  $_ |" } ($genomeLen, $pegCount, @counterValues, $ssCol, $rnaCount));
                                 td({ class => $numStyle }, $genomeLen),  
                                 td({ class => $numStyle }, $pegCount),  
                                 td({ class => $counterStyle }, \@counterValues),  
                                 td({ class => $numStyle }, $ssCol),  
                                 td({ class => $numStyle }, $rnaCount),  
                                 );  
245                  # Put it in the row hash.                  # Put it in the row hash.
246                  $rows{$genomeName} = $rowHtml;                  $rows{$genomeName} = $rowHtml;
247              }              }
# Line 314  Line 254 
254              # Loop through the rows.              # Loop through the rows.
255              for my $rowID (sort keys %rows) {              for my $rowID (sort keys %rows) {
256                  # Format the row.                  # Format the row.
257                  print GROUPFILE Tr( { class => $rowStyle[$rowType] }, $rows{$rowID} ) . "\n";              push @outputLines, $rows{$rowID};
                 # Flip the row type.  
                 $rowType = 1 - $rowType;  
258                  # Count the row.                  # Count the row.
259                  $rowCount++;                  $rowCount++;
260              }              }
261              # All done, terminate the table and close the file.          # All done, write the Wiki Page.
262              print GROUPFILE "</table>\n";          my $rc = $wiki->Save($outPageName, $outputWeb, 'OrganismDataSummariesStats', join("\n", @outputLines));
             close GROUPFILE;  
263              Trace("$rowCount genomes processed.") if T(2);              Trace("$rowCount genomes processed.") if T(2);
264            if (! $rc) {
265                Confess("Error saving $outPageName: $wiki->{error}");
266            }
267              # Now save the group totals.              # Now save the group totals.
268              $summaries{$groupID} = \%groupTotals;              $summaries{$groupID} = \%groupTotals;
269          }          }
270          # Now produce the summary table.          # Now produce the summary table.
271          my $sumFileName = "stats-groups.inc";      my $sumPageName = "OrganismDataSummariesStats";
272          Open(\*SUMFILE, ">$targetDir/$sumFileName");      my @sumLines = ();
273          # Start the table.      # Start the table.  Asterisks make a cell a column header. An extra space at the front right-justifies it.
274          print SUMFILE "<table class=\"$tableStyle\">\n";      push @sumLines, "| " . join("", map { " *$_* |" } ("Group name", "Genomes")) .
275          # Create the header row.                             join("", map { "  *$_* |"} ("[[FIG.ProteinEncodingGenes][Protein Encoding Genes]] (PEGs)",
         print SUMFILE Tr( { class => 'odd' }, th(["Group name",  
                                                  "Genomes",  
                                                  "Protein Encoding Genes (PEGs)",  
276                                                   "Named genes in subsystems",            # s0                                                   "Named genes in subsystems",            # s0
277                                                   "Named genes not in subsystems",        # n0                                                   "Named genes not in subsystems",        # n0
278                                                   "Hypothetical genes in subsystems",     # s1                                                   "Hypothetical genes in subsystems",     # s1
279                                                   "Hypothetical genes not in subsystems", # n1                                                   "Hypothetical genes not in subsystems", # n1
280                                                   "RNAs",                                                         "RNAs"));
                                                    ])) . "\n";  
         # Set up a flag for the odd-even styling.  
         my $rowFlag = 0;  
281          # Put in the data rows.          # Put in the data rows.
282          for my $groupName (sort keys %summaries) {          for my $groupName (sort keys %summaries) {
283              my $group = $summaries{$groupName};              my $group = $summaries{$groupName};
             # Compute the link for the current group.  
             my $groupLink = a({ href => $sprout->GroupPageName($groupName) }, $groupName);  
284              # Create the table row.              # Create the table row.
285              my $rowHtml = join("",          my $rowHtml = "| [[$groupName]] |" . join("", map { "  " . Tracer::CommaFormat($group->{$_}) . " |" }
286                                 td($groupLink),                                                    ('genomes', 'pegs', @columnTypes, 'RNAs'));
287                                 td({ class => $numStyle }, Tracer::CommaFormat($group->{genomes})),          push @sumLines, $rowHtml;
288                                 td({ class => $numStyle }, Tracer::CommaFormat($group->{pegs})),      }
289                                 td({ class => $counterStyle }, [ map { Tracer::CommaFormat($group->{$_}) } @columnTypes ]),      # Write the page.
290                                 td({ class => $numStyle }, Tracer::CommaFormat($group->{RNAs})),      my $rc = $wiki->Save($sumPageName, $outputWeb, 'WebHome', join("\n", @sumLines));
                               );  
             print SUMFILE Tr( { class => $rowStyle[$rowFlag] }, $rowHtml ) . "\n";  
             # Flip the row style.  
             $rowFlag = 1 - $rowFlag;  
         }  
         # Terminate the table and close the file.  
         print SUMFILE "</table>\n";  
         close SUMFILE;  
291          # We're all done.          # We're all done.
292          Trace("Processing complete.") if T(2);          Trace("Processing complete.") if T(2);
     }  
293  };  };
294  if ($@) {  if ($@) {
295      Trace("Stats failed with error: $@") if T(0);      Trace("Stats failed with error: $@") if T(0);

Legend:
Removed from v.1.30  
changed lines
  Added in v.1.32

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3