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revision 1.11, Wed Feb 21 13:20:37 2007 UTC revision 1.22, Mon Mar 16 00:24:23 2009 UTC
# Line 4  Line 4 
4    
5      use strict;      use strict;
6      use Tracer;      use Tracer;
7      use SearchHelper;      use CGI qw(-nosticky);
     use CGI;  
8      use HTML;      use HTML;
9      use Sprout;      use Sprout;
10      use Time::HiRes;      use Time::HiRes;
11      use FIGRules;      use FIGRules;
12        use RHFeatures;
13      our @ISA = qw(SearchHelper);      use base 'SearchHelper';
14    
15  =head1 Gene Discrimination Feature Search Helper  =head1 Gene Discrimination Feature Search Helper
16    
# Line 68  Line 67 
67    
68  =head3 Form  =head3 Form
69    
70  C<< my $html = $shelp->Form(); >>      my $html = $shelp->Form();
71    
72  Generate the HTML for a form to request a new search.  Generate the HTML for a form to request a new search.
73    
# Line 95  Line 94 
94      my $cutoff = $cgi->param('cutoff') || "1e-10";      my $cutoff = $cgi->param('cutoff') || "1e-10";
95      my $statistical = $cgi->param('statistical') || 1;      my $statistical = $cgi->param('statistical') || 1;
96      my $showMatch = $cgi->param('showMatch') || 0;      my $showMatch = $cgi->param('showMatch') || 0;
97        my $useSims = $cgi->param('useSims') || 0;
98        my $pegsOnly = $cgi->param('pegsOnly') || 1;
99      # Now we build the table rows.      # Now we build the table rows.
100      my @rows = ();      my @rows = ();
101      # First we have the given genome.      # First we have the given genome.
102      push @rows, $cgi->Tr($cgi->td({valign => "top"}, "Reference Genome"),      push @rows, CGI::Tr(CGI::td({valign => "top"}, "Reference Genome"),
103                           $cgi->td({colspan => 2}, $givenMenu));                           CGI::td({colspan => 2}, $givenMenu));
104      # Now show the target and exclusion menus.      # Now show the target and exclusion menus.
105      push @rows, $cgi->Tr($cgi->td({valign => "top"}, "Inclusion Genomes (Set 1)"),      push @rows, CGI::Tr(CGI::td({valign => "top"}, "Inclusion Genomes (Set 1)"),
106                           $cgi->td({colspan => 2}, $targetMenu));                           CGI::td({colspan => 2}, $targetMenu));
107      push @rows, $cgi->Tr($cgi->td({valign => "top"}, "Exclusion Genomes (Set 2)"),      push @rows, CGI::Tr(CGI::td({valign => "top"}, "Exclusion Genomes (Set 2)"),
108                           $cgi->td({colspan => 2}, $excludeMenu));                           CGI::td({colspan => 2}, $excludeMenu));
109      # Next, the numeric parameters.      # Next, the tuning parameters.
110      push @rows, $cgi->Tr($cgi->td("Commonality"),      push @rows, CGI::Tr(CGI::td("Commonality"),
111                           $cgi->td($cgi->textfield(-name => 'commonality',                           CGI::td(CGI::textfield(-name => 'commonality',
112                                                    -value => $commonality,                                                    -value => $commonality,
113                                                    -size => 5))),                                                    -size => 5))),
114                  $cgi->Tr($cgi->td(), $cgi->td(join(" ",                  CGI::Tr(CGI::td(), CGI::td(join(" ",
115                                    $cgi->checkbox(-name => 'statistical',                                    CGI::checkbox(-name => 'statistical',
116                                                   -checked => $statistical,                                                   -checked => $statistical,
117                                                   -value => 1,                                                   -value => 1,
118                                                   -label => 'Use Statistical Algorithm')),                                                   -label => 'Use Statistical Algorithm') .
119                                    $cgi->checkbox(-name => 'showMatch',                                    SearchHelper::Hint("SigGenes", 24),
120                                      CGI::checkbox(-name => 'useSims',
121                                                     -checked => $useSims,
122                                                     -value => 1,
123                                                     -label => 'Use Similarities') .
124                                      SearchHelper::Hint("SigGenes", 25)))),
125                    CGI::Tr(CGI::td(), CGI::td(join(" ",
126                                      CGI::checkbox(-name => 'showMatch',
127                                                   -checked => $showMatch,                                                   -checked => $showMatch,
128                                                   -value => 1,                                                   -value => 1,
129                                                   -label => 'Show Matching Genes')));                                                   -label => 'Show Matching Genes') .
130      push @rows, $cgi->Tr($cgi->td("Cutoff"),                                    SearchHelper::Hint("SigGenes", 26)))),
131                           $cgi->td($cgi->textfield(-name => 'cutoff',                  CGI::Tr(CGI::td("Cutoff"),
132                             CGI::td(CGI::textfield(-name => 'cutoff',
133                                                    -value => $cutoff,                                                    -value => $cutoff,
134                                                    -size => 5)));                                                    -size => 5)));
135      # Next, the feature filter rows.      # Next, the feature filter rows.
136      push @rows, $self->FeatureFilterRows();      push @rows, RHFeatures::WordSearchRow($self);
137        push @rows, RHFeatures::FeatureFilterFormRows($self);
138      # Finally, the submit button.      # Finally, the submit button.
139      push @rows, $self->SubmitRow();      push @rows, $self->SubmitRow();
140      # Create the table.      # Create the table.
# Line 137  Line 147 
147    
148  =head3 Find  =head3 Find
149    
150  C<< my $resultCount = $shelp->Find(); >>      my $resultCount = $shelp->Find();
151    
152  Conduct a search based on the current CGI query parameters. The search results will  Conduct a search based on the current CGI query parameters. The search results will
153  be written to the session cache file and the number of results will be  be written to the session cache file and the number of results will be
# Line 155  Line 165 
165      # Declare the return variable. If it remains undefined, the caller will      # Declare the return variable. If it remains undefined, the caller will
166      # assume there was an error.      # assume there was an error.
167      my $retVal;      my $retVal;
     # Denote the extra columns go at the end.  
     $self->SetExtraPos(1);  
168      # Create the timers.      # Create the timers.
169      my ($saveTime, $loopCounter, $bbhTimer, $putTimer, $queryTimer) = (0, 0, 0, 0, 0);      my ($saveTime, $loopCounter, $bbhTimer, $putTimer, $queryTimer) = (0, 0, 0, 0, 0);
170      # Validate the numeric parameters.      # Validate the numeric parameters.
# Line 171  Line 179 
179      } elsif ($cutoff > 1) {      } elsif ($cutoff > 1) {
180          $self->SetMessage("Cutoff cannot be greater than 1.");          $self->SetMessage("Cutoff cannot be greater than 1.");
181      } else {      } else {
182            # Get the result helper.
183            my $rhelp = RHFeatures->new($self);
184            # Set up the default columns.
185            $self->DefaultColumns($rhelp);
186            # Add the score at the end.
187            $rhelp->AddExtraColumn(score => undef, title => 'Score', style => 'rightAlign', download => 'num');
188            # Find out if we need to show matching genes.
189            my $showMatch = $cgi->param('showMatch') || 0;
190            # If we do, add a column for them at the front.
191            if ($showMatch) {
192                $rhelp->AddExtraColumn(matches => 0, title => 'Matches', style => 'leftAlign', download => 'list');
193            }
194            # Only proceed if the filtering parameters are valid.
195            if ($rhelp->Valid()) {
196          # Now we need to gather and validate the genome sets.          # Now we need to gather and validate the genome sets.
197                $self->PrintLine("Gathering the target genomes.  ");
198          my ($givenGenomeID) = $self->GetGenomes('given');          my ($givenGenomeID) = $self->GetGenomes('given');
199                Trace("Given genome is $givenGenomeID.") if T(3);
200          my %targetGenomes = map { $_ => 1 } $self->GetGenomes('target');          my %targetGenomes = map { $_ => 1 } $self->GetGenomes('target');
201                Trace("Target genomes are " . join(", ", sort keys %targetGenomes) . ".") if T(3);
202                $self->PrintLine("Gathering the exclusion genomes.  ");
203          my %exclusionGenomes = map { $_ => 1 } $self->GetGenomes('exclusion');          my %exclusionGenomes = map { $_ => 1 } $self->GetGenomes('exclusion');
204                Trace("Exclusion genomes are " . join(", ", sort keys %exclusionGenomes) . ".") if T(3);
205                $self->PrintLine("Validating the genome sets.<br />");
206          # Insure the given genome is not in the exclusion set.          # Insure the given genome is not in the exclusion set.
207          if ($exclusionGenomes{$givenGenomeID}) {          if ($exclusionGenomes{$givenGenomeID}) {
208              $self->SetMessage("The given genome ($givenGenomeID) cannot be in the exclusion set.");              $self->SetMessage("The given genome ($givenGenomeID) cannot be in the exclusion set.");
209          } else {          } else {
210                    # Start the output session.
211                    $self->OpenSession($rhelp);
212              # Insure the given genome is in the target set.              # Insure the given genome is in the target set.
213              $targetGenomes{$givenGenomeID} = 1                  $targetGenomes{$givenGenomeID} = 1;
214          }                  Trace("$givenGenomeID added to target set.") if T(3);
215          # Find out if we want to use a statistical analysis.          # Find out if we want to use a statistical analysis.
216          my $statistical = $cgi->param('statistical') || 1;          my $statistical = $cgi->param('statistical') || 1;
         # Find out if we need to show matching genes.  
         my $showMatch = $cgi->param('showMatch') || 0;  
217          # Denote we have not yet found any genomes.          # Denote we have not yet found any genomes.
218          $retVal = 0;          $retVal = 0;
219          # Compute the list of genomes of interest.          # Compute the list of genomes of interest.
220          my @allGenomes = (keys %exclusionGenomes, keys %targetGenomes);          my @allGenomes = (keys %exclusionGenomes, keys %targetGenomes);
221          # Get the BBH matrix.                  # Get the peg matrix.
222                    Trace("Requesting matrix.") if T(3);
223          $saveTime = time();          $saveTime = time();
224          my %bbhMatrix = $sprout->BBHMatrix($givenGenomeID, $cutoff, @allGenomes);                  my $bbhMatrix;
225                    if (! $cgi->param('useSims')) {
226                        # Here we are using BBHs, which are fast enough to do in one gulp.
227                        $self->PrintLine("Requesting bidirectional best hits.  ");
228                        $bbhMatrix = $sprout->BBHMatrix($givenGenomeID, $cutoff, @allGenomes);
229                    } else {
230                        # Here we are using similarities, which are much more complicated.
231                        $self->PrintLine("Requesting similarities.<br />");
232                        # Create a filtering matrix for the results. We only want to keep PEGs in the
233                        # specified target and exclusion genomes.
234                        my %keepGenomes = map { $_ => 1 } @allGenomes;
235                        # Loop through the given genome's features.
236                        my @features = $sprout->FeaturesOf($givenGenomeID);
237                        for my $fid (@features) {
238                            $self->PrintLine("Retrieving similarities for $fid.  ");
239                            # Get this feature's similarities.
240                            my $simList = $sprout->Sims($fid, 1000, $cutoff, 'fig');
241                            my $simCount = scalar @{$simList};
242                            $self->PrintLine("Raw similarity count: $simCount.  ");
243                            # Create the matrix hash for this feature.
244                            $bbhMatrix->{$fid} = {};
245                            # Now we need to filter out the similarities that don't land on the target genome.
246                            $simCount = 0;
247                            for my $sim (@{$simList}) {
248                                # Insure this similarity lands on a target genome.
249                                my $genomeID2 = $sprout->GenomeOf($sim->id2);
250                                if ($keepGenomes{$genomeID2}) {
251                                    # Here we're keeping the similarity, so we put it in this feature's hash.
252                                    $bbhMatrix->{$fid}->{$sim->id2} = $sim->psc;
253                                    $simCount++;
254                                }
255                            }
256                            $self->PrintLine("Similarities retained: $simCount.<br />");
257                        }
258                    }
259          $bbhTimer += time() - $saveTime;          $bbhTimer += time() - $saveTime;
260                    $self->PrintLine("Time to build matrix: $bbhTimer seconds.<br />");
261                    Trace("Matrix built.") if T(3);
262          # Create a feature query object to loop through the chosen features of the given          # Create a feature query object to loop through the chosen features of the given
263          # genome.          # genome.
264          Trace("Creating feature query.") if T(3);          Trace("Creating feature query.") if T(3);
265          $saveTime = time();          $saveTime = time();
266          my $fquery = FeatureQuery->new($self, $givenGenomeID);                  my $fquery = $rhelp->GetQuery($givenGenomeID);
267          $queryTimer += time() - $saveTime;          $queryTimer += time() - $saveTime;
268          # Get the sizes of the two sets. This information is useful in computing commonality.          # Get the sizes of the two sets. This information is useful in computing commonality.
269          my $targetSetSize = scalar keys %targetGenomes;          my $targetSetSize = scalar keys %targetGenomes;
# Line 208  Line 273 
273          while (! $done) {          while (! $done) {
274              # Get the next feature.              # Get the next feature.
275              $saveTime = time();              $saveTime = time();
276              my $record = $fquery->Fetch();                      my $record = $rhelp->Fetch($fquery);
277              $queryTimer += time() - $saveTime;              $queryTimer += time() - $saveTime;
278              if (! $record) {              if (! $record) {
279                  $done = 1;                  $done = 1;
280              } else {              } else {
281                  # Get the feature's ID.                  # Get the feature's ID.
282                  my $fid = $fquery->FID();                          my $fid = $record->PrimaryValue('Feature(id)');
283                  Trace("Processing feature $fid.") if T(4);                          Trace("Checking feature $fid.") if T(4);
284                  # Get its list of BBHs. The list is actually a hash mapping each BBH to its                          $self->PrintLine("Checking feature $fid.<br />");
285                  # score. All we care about, however, are the BBHs themselves.                          # Get its list of matching genes. The list is actually a hash mapping each matched gene to its
286                  my $bbhList = $bbhMatrix{$fid};                          # score. All we care about, however, are the matches themselves.
287                            my $bbhList = $bbhMatrix->{$fid};
288                  # We next wish to loop through the BBH IDs, counting how many are in each of the                  # We next wish to loop through the BBH IDs, counting how many are in each of the
289                  # sets. If a genome occurs twice, we only want to count the first occurrence, so                  # sets. If a genome occurs twice, we only want to count the first occurrence, so
290                  # we have a hash of genomes we've already seen. The hash will map each gene ID                  # we have a hash of genomes we've already seen. The hash will map each gene ID
# Line 232  Line 298 
298                  # Denote that we're in our own genome.                  # Denote that we're in our own genome.
299                  $alreadySeen{$givenGenomeID} = 0;                  $alreadySeen{$givenGenomeID} = 0;
300                  my $targetCount = 1;                  my $targetCount = 1;
301                  # Loop through the BBHs.                          # Loop through the BBHs/Sims.
302                  for my $bbhPeg (keys %{$bbhList}) {                  for my $bbhPeg (keys %{$bbhList}) {
303                      # Get the genome ID. We want to find out if this genome is new.                      # Get the genome ID. We want to find out if this genome is new.
304                      my ($genomeID) = FIGRules::ParseFeatureID($bbhPeg);                              my $genomeID = $sprout->GenomeOf($bbhPeg);
305                      if (! exists $alreadySeen{$genomeID}) {                      if (! exists $alreadySeen{$genomeID}) {
306                          # It's new, so we check to see which set it's in.                          # It's new, so we check to see which set it's in.
307                          if ($targetGenomes{$genomeID}) {                          if ($targetGenomes{$genomeID}) {
# Line 272  Line 338 
338                      # If the two differentials are greater than one, we keep this feature.                      # If the two differentials are greater than one, we keep this feature.
339                      $score = $inD + $outD;                      $score = $inD + $outD;
340                      $okFlag = ($score > 1);                      $okFlag = ($score > 1);
341                                # Subtract 1 from the score so it looks like the commonality score.
342                                $score -= 1.0;
343                  } else {                  } else {
344                      # Check to see if we're common in set 1 and not in set 2.                      # Check to see if we're common in set 1 and not in set 2.
345                      my $score1 = IsCommon($targetCount, $targetSetSize, $commonality);                      my $score1 = IsCommon($targetCount, $targetSetSize, $commonality);
346                      my $score2 = IsCommon($exclusionCount, $exclusionSetSize, $commonality);                      my $score2 = IsCommon($exclusionCount, $exclusionSetSize, $commonality);
347                      if ($score1 && ! $score2) {                      if ($score1 && ! $score2) {
348                          # We satisfy the criterion, so we put this feature to the output. The                          # We satisfy the criterion, so we put this feature to the output. The
349                          # score is normalize to a range similar to the scores in the statistical                                  # score is essentially $score1, since $score2 is zero.
350                          # method.                                  $score = $score1;
                         $score = $score1 + (1 - $score2);  
351                          $okFlag = 1;                          $okFlag = 1;
352                      }                      }
353                  }                  }
354                  if ($okFlag) {                  if ($okFlag) {
355                      # Put this feature to the output. We have one or two extra columns.                      # Put this feature to the output. We have one or two extra columns.
356                      # First we store the score.                      # First we store the score.
357                      $fquery->AddExtraColumns(score => sprintf("%.3f",$score));                              $rhelp->PutExtraColumns(score => sprintf("%0.3f",$score));
358                      # Next we add the list of matching genes, but only if "showMatch" is specified.                      # Next we add the list of matching genes, but only if "showMatch" is specified.
359                      if ($showMatch) {                      if ($showMatch) {
360                          # The matching genes are in the hash "genesMatching".                          # The matching genes are in the hash "genesMatching".
# Line 295  Line 362 
362                          # We need to linkify them.                          # We need to linkify them.
363                          my $genesHTML = join(", ", map { HTML::fid_link($cgi, $_) } @genes);                          my $genesHTML = join(", ", map { HTML::fid_link($cgi, $_) } @genes);
364                          # Now add them as an extra column.                          # Now add them as an extra column.
365                          $fquery->AddExtraColumns(matches => $genesHTML);                                  $rhelp->PutExtraColumns(matches => $genesHTML);
366                      }                      }
367                                # Compute a sort key from the feature data and the score.
368                                my $sort = $rhelp->SortKey($record, sprintf("%0.3f", 1 - $score));
369                                # Output the feature.
370                      $saveTime = time();                      $saveTime = time();
371                      $self->PutFeature($fquery);                              $rhelp->PutData($sort, $fid, $record);
372                      $putTimer += time() - $saveTime;                      $putTimer += time() - $saveTime;
373                      # Increase the result count.                      # Increase the result count.
374                      $retVal++;                      $retVal++;
# Line 315  Line 385 
385          $self->CloseSession();          $self->CloseSession();
386          $putTimer += time() - $saveTime;          $putTimer += time() - $saveTime;
387      }      }
388            }
389        }
390      # Trace the timers.      # Trace the timers.
391      Trace("Time spent: Put = $putTimer, Query = $queryTimer, BBH = $bbhTimer.") if T(3);      Trace("Time spent: Put = $putTimer, Query = $queryTimer, BBH = $bbhTimer.") if T(3);
392      # Return the result count.      # Return the result count.
# Line 323  Line 395 
395    
396  =head3 Description  =head3 Description
397    
398  C<< my $htmlText = $shelp->Description(); >>      my $htmlText = $shelp->Description();
399    
400  Return a description of this search. The description is used for the table of contents  Return a description of this search. The description is used for the table of contents
401  on the main search tools page. It may contain HTML, but it should be character-level,  on the main search tools page. It may contain HTML, but it should be character-level,
# Line 338  Line 410 
410      return "Search for genes that are common to a group of organisms or that discriminate between two groups of organisms.";      return "Search for genes that are common to a group of organisms or that discriminate between two groups of organisms.";
411  }  }
412    
413    =head3 SearchTitle
414    
415        my $titleHtml = $shelp->SearchTitle();
416    
417    Return the display title for this search. The display title appears above the search results.
418    If no result is returned, no title will be displayed. The result should be an html string
419    that can be legally put inside a block tag such as C<h3> or C<p>.
420    
421    =cut
422    
423    sub SearchTitle {
424        # Get the parameters.
425        my ($self) = @_;
426        # Compute the title. We extract the relevant clues from the query parameters.
427        my $cgi = $self->Q();
428        my $type = ($cgi->param('useSims') ? "Similarities" : "Bidirectional Best Hits");
429        my $style = ($cgi->param('exclusion') ? "Discriminating" : "Common");
430        my $retVal = "$style Genes using $type";
431        # Return it.
432        return $retVal;
433    }
434    
435  =head2 Internal Utilities  =head2 Internal Utilities
436    
437  =head3 IsCommon  =head3 IsCommon
438    
439  C<< my $score = SHSigGenes::IsCommon($count, $size, $commonality); >>      my $score = SHSigGenes::IsCommon($count, $size, $commonality);
440    
441  Return the match score if a specified count indicates a gene is common in a specified set  Return the match score if a specified count indicates a gene is common in a specified set
442  and 0 otherwise. Commonality is computed by dividing the count by the size of the set and  and 0 otherwise. Commonality is computed by dividing the count by the size of the set and

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