[Bio] / FigKernelScripts / TransactFeatures.pl Repository:
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revision 1.13, Mon Aug 15 21:36:28 2005 UTC revision 1.14, Thu Sep 1 09:39:31 2005 UTC
# Line 7  Line 7 
7  a command. The second specifies a directory full of transaction files. The third  a command. The second specifies a directory full of transaction files. The third
8  specifies a file that tells us which feature IDs are available for each organism.  specifies a file that tells us which feature IDs are available for each organism.
9    
10  C<TransactFeatures> I<[options]> I<command> I<transactionDirectory> I<idFile>  C<TransactFeatures> [I<options>] I<command> I<transactionDirectory> I<idFile>
11    
12  The supported commands are  The supported commands are
13    
# Line 28  Line 28 
28    
29  =item process  =item process
30    
31  Process the transactions and update the FIG data store. This will also create  Process the transactions and update the FIG data store. This will also update
32  a copy of each transaction file in which the pseudo-IDs have been replaced by  the NR file and queue features for similarity generation.
 real IDs.  
33    
34  =item annotate  =item fudge
35    
36  Annotate the features created by the transactions so as to indicate how they were  Convert transactions that have already been applied to new transactions that can
37  derived.  be used to test the transaction processor.
   
 =item check  
   
 Verify that the locations and translations of the new and changed features are  
 correct.  
   
 =item fix  
   
 Fix the locations and translations of the new and changed features.  
   
 =item aliasMove  
   
 Move the aliases from the old features to the ones that replaced them.  
   
 =item attribute  
   
 Move the attributes from the old features to the ones that replaced them.  
   
 =item attributeCheck  
   
 Same as C<attribute>, but no changes are made to the database.  
38    
39  =back  =back
40    
# Line 196  Line 174 
174  use TransactionProcessor;  use TransactionProcessor;
175  use ApplyTransactions;  use ApplyTransactions;
176  use CountTransactions;  use CountTransactions;
177  use AnnotateTransactions;  use FudgeTransactions;
 use AttributeTransactions;  
 use FixTransactions;  
 use MoveAliases;  
178    
179  # Get the command-line options.  # Get the command-line options.
180  my ($options, @parameters) = Tracer::ParseCommand({ trace => 3, sql => 0, safe => 0, noAlias => 0,  my ($options, @parameters) = Tracer::ParseCommand({ trace => 3, sql => 0, safe => 0, noAlias => 0,
# Line 222  Line 197 
197      $controlBlock = CountTransactions->new($options, $mainCommand, @parameters);      $controlBlock = CountTransactions->new($options, $mainCommand, @parameters);
198  } elsif ($mainCommand eq 'process') {  } elsif ($mainCommand eq 'process') {
199      $controlBlock = ApplyTransactions->new($options, $mainCommand, @parameters);      $controlBlock = ApplyTransactions->new($options, $mainCommand, @parameters);
200  } elsif ($mainCommand eq 'annotate') {  } elsif ($mainCommand eq 'fudge') {
201      $controlBlock = AnnotateTransactions->new($options, $mainCommand, @parameters);      $controlBlock = FudgeTransactions->new($options, $mainCommand, @parameters);
 } elsif ($mainCommand eq 'fix' || $mainCommand eq 'check') {  
     $controlBlock = FixTransactions->new($options, $mainCommand, @parameters);  
 } elsif ($mainCommand eq 'aliasmove') {  
     $controlBlock = MoveAliases->new($options, $mainCommand, @parameters);  
 } elsif ($mainCommand eq 'attribute') {  
     $controlBlock = AttributeTransactions->new($options, $mainCommand, @parameters);  
 } elsif ($mainCommand eq 'attributecheck') {  
     $controlBlock = AttributeTransactions->new($options, $mainCommand, @parameters);  
202  } else {  } else {
203      Confess("Invalid command \"$mainCommand\" specified on command line.");      Confess("Invalid command \"$mainCommand\" specified on command line.");
204  }  }
# Line 304  Line 271 
271                  }                  }
272                  $controlBlock->IncrementStat($command);                  $controlBlock->IncrementStat($command);
273              }              }
274                # Close the transaction input file.
275                close TRANS;
276              # Terminate processing for this genome.              # Terminate processing for this genome.
277              my $orgStats = $controlBlock->EndGenome();              my $orgStats = $controlBlock->EndGenome();
278              Trace("Statistics for $genomeID\n\n" . $orgStats->Show() . "\n") if T(3);              Trace("Statistics for $genomeID\n\n" . $orgStats->Show() . "\n") if T(3);
             # Close the transaction input file.  
             close TRANS;  
279          }          }
280      }      }
281      # Terminate processing.      # Terminate processing.

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