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revision 1.11, Wed Feb 21 13:20:37 2007 UTC revision 1.16, Mon Jul 16 20:04:51 2007 UTC
# Line 4  Line 4 
4    
5      use strict;      use strict;
6      use Tracer;      use Tracer;
     use SearchHelper;  
7      use CGI;      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 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.
# Line 105  Line 106 
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,
# Line 114  Line 115 
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                                      SearchHelper::Hint("When two sets of genomees are specified, check this " .
120                                                         "box to use a statistical algorithm designed " .
121                                                         "specifically to choose differentiating genes. " .
122                                                         "This box has no effect when looking for genes " .
123                                                         "in common."),
124                                      $cgi->checkbox(-name => 'useSims',
125                                                     -checked => $useSims,
126                                                     -value => 1,
127                                                     -label => 'Use Similarities') .
128                                      SearchHelper::Hint("Normally, Bidirectional Best Hits are used to " .
129                                                         "find matching genes. Check this box to use " .
130                                                         "similarities instead.")))),
131                    $cgi->Tr($cgi->td(), $cgi->td(join(" ",
132                                    $cgi->checkbox(-name => 'showMatch',                                    $cgi->checkbox(-name => 'showMatch',
133                                                   -checked => $showMatch,                                                   -checked => $showMatch,
134                                                   -value => 1,                                                   -value => 1,
135                                                   -label => 'Show Matching Genes')));                                                   -label => 'Show Matching Genes') .
136      push @rows, $cgi->Tr($cgi->td("Cutoff"),                                    SearchHelper::Hint("Check this button to display the genes matching " .
137                                                         "each gene displayed in the results.")))),
138                    $cgi->Tr($cgi->td("Cutoff"),
139                           $cgi->td($cgi->textfield(-name => 'cutoff',                           $cgi->td($cgi->textfield(-name => 'cutoff',
140                                                    -value => $cutoff,                                                    -value => $cutoff,
141                                                    -size => 5)));                                                    -size => 5)));
142      # Next, the feature filter rows.      # Next, the feature filter rows.
143      push @rows, $self->FeatureFilterRows();      push @rows, RHFeatures::WordSearchRow($self);
144        push @rows, RHFeatures::FeatureFilterFormRows($self);
145      # Finally, the submit button.      # Finally, the submit button.
146      push @rows, $self->SubmitRow();      push @rows, $self->SubmitRow();
147      # Create the table.      # Create the table.
# Line 155  Line 172 
172      # Declare the return variable. If it remains undefined, the caller will      # Declare the return variable. If it remains undefined, the caller will
173      # assume there was an error.      # assume there was an error.
174      my $retVal;      my $retVal;
     # Denote the extra columns go at the end.  
     $self->SetExtraPos(1);  
175      # Create the timers.      # Create the timers.
176      my ($saveTime, $loopCounter, $bbhTimer, $putTimer, $queryTimer) = (0, 0, 0, 0, 0);      my ($saveTime, $loopCounter, $bbhTimer, $putTimer, $queryTimer) = (0, 0, 0, 0, 0);
177      # Validate the numeric parameters.      # Validate the numeric parameters.
# Line 171  Line 186 
186      } elsif ($cutoff > 1) {      } elsif ($cutoff > 1) {
187          $self->SetMessage("Cutoff cannot be greater than 1.");          $self->SetMessage("Cutoff cannot be greater than 1.");
188      } else {      } else {
189            # Get the result helper.
190            my $rhelp = RHFeatures->new($self);
191            # Set up the default columns.
192            $self->DefaultColumns($rhelp);
193            # Add the score at the end.
194            $rhelp->AddExtraColumn(score => undef, title => 'Score', style => 'rightAlign', download => 'num');
195            # Find out if we need to show matching genes.
196            my $showMatch = $cgi->param('showMatch') || 0;
197            # If we do, add a column for them at the front.
198            if ($showMatch) {
199                $rhelp->AddExtraColumn(matches => 0, title => 'Matches', style => 'leftAlign', download => 'list');
200            }
201            # Only proceed if the filtering parameters are valid.
202            if ($rhelp->Valid()) {
203                # Start the output session.
204                $self->OpenSession($rhelp);
205          # Now we need to gather and validate the genome sets.          # Now we need to gather and validate the genome sets.
206                $self->PrintLine("Gathering the target genomes.  ");
207          my ($givenGenomeID) = $self->GetGenomes('given');          my ($givenGenomeID) = $self->GetGenomes('given');
208          my %targetGenomes = map { $_ => 1 } $self->GetGenomes('target');          my %targetGenomes = map { $_ => 1 } $self->GetGenomes('target');
209                $self->PrintLine("Gathering the exclusion genomes.  ");
210          my %exclusionGenomes = map { $_ => 1 } $self->GetGenomes('exclusion');          my %exclusionGenomes = map { $_ => 1 } $self->GetGenomes('exclusion');
211                $self->PrintLine("Validating the genome sets.<br />");
212          # Insure the given genome is not in the exclusion set.          # Insure the given genome is not in the exclusion set.
213          if ($exclusionGenomes{$givenGenomeID}) {          if ($exclusionGenomes{$givenGenomeID}) {
214              $self->SetMessage("The given genome ($givenGenomeID) cannot be in the exclusion set.");              $self->SetMessage("The given genome ($givenGenomeID) cannot be in the exclusion set.");
215          } else {          } else {
216              # Insure the given genome is in the target set.              # Insure the given genome is in the target set.
217              $targetGenomes{$givenGenomeID} = 1                  $targetGenomes{$givenGenomeID} = 1;
218          }          }
219          # Find out if we want to use a statistical analysis.          # Find out if we want to use a statistical analysis.
220          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;  
221          # Denote we have not yet found any genomes.          # Denote we have not yet found any genomes.
222          $retVal = 0;          $retVal = 0;
223          # Compute the list of genomes of interest.          # Compute the list of genomes of interest.
224          my @allGenomes = (keys %exclusionGenomes, keys %targetGenomes);          my @allGenomes = (keys %exclusionGenomes, keys %targetGenomes);
225          # Get the BBH matrix.              # Get the peg matrix.
226                Trace("Requesting matrix.") if T(3);
227          $saveTime = time();          $saveTime = time();
228          my %bbhMatrix = $sprout->BBHMatrix($givenGenomeID, $cutoff, @allGenomes);              my %bbhMatrix;
229                if (! $cgi->param('useSims')) {
230                    # Here we are using BBHs, which are fast enough to do in one gulp.
231                    $self->PrintLine("Requesting bidirectional best hits.  ");
232                    %bbhMatrix = $sprout->BBHMatrix($givenGenomeID, $cutoff, @allGenomes);
233                } else {
234                    # Here we are using similarities, which are much more complicated.
235                    $self->PrintLine("Requesting similarities.<br />");
236                    # Create a filtering matrix for the results. We only want to keep PEGs in the
237                    # specified target and exclusion genomes.
238                    my %keepGenomes = map { $_ => 1 } @allGenomes;
239                    # Loop through the given genome's features.
240                    my @features = $sprout->FeaturesOf($givenGenomeID);
241                    for my $fid (@features) {
242                        $self->PrintLine("Retrieving similarities for $fid.  ");
243                        # Get this feature's similarities.
244                        my $simList = $sprout->Sims($fid, 1000, $cutoff, 'fig');
245                        my $simCount = scalar @{$simList};
246                        $self->PrintLine("Raw similarity count: $simCount.  ");
247                        # Create the matrix hash for this feature.
248                        $bbhMatrix{$fid} = {};
249                        # Now we need to filter out the similarities that don't land on the target genome.
250                        $simCount = 0;
251                        for my $sim (@{$simList}) {
252                            # Insure this similarity lands on a target genome.
253                            my $genomeID2 = $sprout->GenomeOf($sim->id2);
254                            if ($keepGenomes{$genomeID2}) {
255                                # Here we're keeping the similarity, so we put it in this feature's hash.
256                                $bbhMatrix{$fid}->{$sim->id2} = $sim->psc;
257                                $simCount++;
258                            }
259                        }
260                        $self->PrintLine("Similarities retained: $simCount.<br />");
261                    }
262                }
263          $bbhTimer += time() - $saveTime;          $bbhTimer += time() - $saveTime;
264                $self->PrintLine("Time to build matrix: $bbhTimer seconds.<br />");
265                Trace("Matrix built.") if T(3);
266          # 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
267          # genome.          # genome.
268          Trace("Creating feature query.") if T(3);          Trace("Creating feature query.") if T(3);
269          $saveTime = time();          $saveTime = time();
270          my $fquery = FeatureQuery->new($self, $givenGenomeID);              my $fquery = $rhelp->GetQuery($givenGenomeID);
271          $queryTimer += time() - $saveTime;          $queryTimer += time() - $saveTime;
272          # 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.
273          my $targetSetSize = scalar keys %targetGenomes;          my $targetSetSize = scalar keys %targetGenomes;
# Line 208  Line 277 
277          while (! $done) {          while (! $done) {
278              # Get the next feature.              # Get the next feature.
279              $saveTime = time();              $saveTime = time();
280              my $record = $fquery->Fetch();                  my $record = $rhelp->Fetch($fquery);
281              $queryTimer += time() - $saveTime;              $queryTimer += time() - $saveTime;
282              if (! $record) {              if (! $record) {
283                  $done = 1;                  $done = 1;
284              } else {              } else {
285                  # Get the feature's ID.                  # Get the feature's ID.
286                  my $fid = $fquery->FID();                      my $fid = $record->PrimaryValue('Feature(id)');
287                  Trace("Processing feature $fid.") if T(4);                      Trace("Checking feature $fid.") if T(4);
288                  # Get its list of BBHs. The list is actually a hash mapping each BBH to its                      $self->PrintLine("Checking feature $fid.<br />");
289                  # 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
290                        # score. All we care about, however, are the matches themselves.
291                  my $bbhList = $bbhMatrix{$fid};                  my $bbhList = $bbhMatrix{$fid};
292                  # 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
293                  # 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
# Line 232  Line 302 
302                  # Denote that we're in our own genome.                  # Denote that we're in our own genome.
303                  $alreadySeen{$givenGenomeID} = 0;                  $alreadySeen{$givenGenomeID} = 0;
304                  my $targetCount = 1;                  my $targetCount = 1;
305                  # Loop through the BBHs.                      # Loop through the BBHs/Sims.
306                  for my $bbhPeg (keys %{$bbhList}) {                  for my $bbhPeg (keys %{$bbhList}) {
307                      # 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.
308                      my ($genomeID) = FIGRules::ParseFeatureID($bbhPeg);                          my $genomeID = $sprout->GenomeOf($bbhPeg);
309                      if (! exists $alreadySeen{$genomeID}) {                      if (! exists $alreadySeen{$genomeID}) {
310                          # 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.
311                          if ($targetGenomes{$genomeID}) {                          if ($targetGenomes{$genomeID}) {
# Line 272  Line 342 
342                      # If the two differentials are greater than one, we keep this feature.                      # If the two differentials are greater than one, we keep this feature.
343                      $score = $inD + $outD;                      $score = $inD + $outD;
344                      $okFlag = ($score > 1);                      $okFlag = ($score > 1);
345                            # Subtract 1 from the score so it looks like the commonality score.
346                            $score -= 1.0;
347                  } else {                  } else {
348                      # 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.
349                      my $score1 = IsCommon($targetCount, $targetSetSize, $commonality);                      my $score1 = IsCommon($targetCount, $targetSetSize, $commonality);
350                      my $score2 = IsCommon($exclusionCount, $exclusionSetSize, $commonality);                      my $score2 = IsCommon($exclusionCount, $exclusionSetSize, $commonality);
351                      if ($score1 && ! $score2) {                      if ($score1 && ! $score2) {
352                          # 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
353                          # score is normalize to a range similar to the scores in the statistical                              # score is essentially $score1, since $score2 is zero.
354                          # method.                              $score = $score1;
                         $score = $score1 + (1 - $score2);  
355                          $okFlag = 1;                          $okFlag = 1;
356                      }                      }
357                  }                  }
358                  if ($okFlag) {                  if ($okFlag) {
359                      # 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.
360                      # First we store the score.                      # First we store the score.
361                      $fquery->AddExtraColumns(score => sprintf("%.3f",$score));                          $rhelp->PutExtraColumns(score => sprintf("%0.3f",$score));
362                      # 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.
363                      if ($showMatch) {                      if ($showMatch) {
364                          # The matching genes are in the hash "genesMatching".                          # The matching genes are in the hash "genesMatching".
# Line 295  Line 366 
366                          # We need to linkify them.                          # We need to linkify them.
367                          my $genesHTML = join(", ", map { HTML::fid_link($cgi, $_) } @genes);                          my $genesHTML = join(", ", map { HTML::fid_link($cgi, $_) } @genes);
368                          # Now add them as an extra column.                          # Now add them as an extra column.
369                          $fquery->AddExtraColumns(matches => $genesHTML);                              $rhelp->PutExtraColumns(matches => $genesHTML);
370                      }                      }
371                            # Compute a sort key from the feature data and the score.
372                            my $sort = $rhelp->SortKey($record, sprintf("%0.3f", 1 - $score));
373                            # Output the feature.
374                      $saveTime = time();                      $saveTime = time();
375                      $self->PutFeature($fquery);                          $rhelp->PutData($sort, $fid, $record);
376                      $putTimer += time() - $saveTime;                      $putTimer += time() - $saveTime;
377                      # Increase the result count.                      # Increase the result count.
378                      $retVal++;                      $retVal++;
# Line 315  Line 389 
389          $self->CloseSession();          $self->CloseSession();
390          $putTimer += time() - $saveTime;          $putTimer += time() - $saveTime;
391      }      }
392        }
393      # Trace the timers.      # Trace the timers.
394      Trace("Time spent: Put = $putTimer, Query = $queryTimer, BBH = $bbhTimer.") if T(3);      Trace("Time spent: Put = $putTimer, Query = $queryTimer, BBH = $bbhTimer.") if T(3);
395      # Return the result count.      # Return the result count.
# Line 338  Line 413 
413      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.";
414  }  }
415    
416    =head3 SearchTitle
417    
418    C<< my $titleHtml = $shelp->SearchTitle(); >>
419    
420    Return the display title for this search. The display title appears above the search results.
421    If no result is returned, no title will be displayed. The result should be an html string
422    that can be legally put inside a block tag such as C<h3> or C<p>.
423    
424    =cut
425    
426    sub SearchTitle {
427        # Get the parameters.
428        my ($self) = @_;
429        # Compute the title. We extract the relevant clues from the query parameters.
430        my $cgi = $self->Q();
431        my $type = ($cgi->param('useSims') ? "Similarities" : "Bidirectional Best Hits");
432        my $style = ($cgi->param('exclusion') ? "Discriminating" : "Common");
433        my $retVal = "$style Genes using $type";
434        # Return it.
435        return $retVal;
436    }
437    
438  =head2 Internal Utilities  =head2 Internal Utilities
439    
440  =head3 IsCommon  =head3 IsCommon

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