[Bio] / FigKernelScripts / TransactFeatures.pl Repository:
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revision 1.8, Fri Aug 12 09:33:50 2005 UTC revision 1.12, Mon Aug 15 21:08:56 2005 UTC
# Line 50  Line 50 
50    
51  Move the aliases from the old features to the ones that replaced them.  Move the aliases from the old features to the ones that replaced them.
52    
53    =item attribute
54    
55    Move the attributes from the old features to the ones that replaced them.
56    
57    =item attributeCheck
58    
59    Same as C<attribute>, but no changes are made to the database.
60    
61  =back  =back
62    
63  =head2 The Transaction File  =head2 The Transaction File
# Line 167  Line 175 
175    
176  Trace SQL commands.  Trace SQL commands.
177    
178    =item start
179    
180    ID of the first genome to process. This allows restarting a transaction run that failed
181    in the middle. The default is to run all transaction files.
182    
183  =back  =back
184    
185  =cut  =cut
# Line 184  Line 197 
197  use ApplyTransactions;  use ApplyTransactions;
198  use CountTransactions;  use CountTransactions;
199  use AnnotateTransactions;  use AnnotateTransactions;
200    use AttributeTransactions;
201  use FixTransactions;  use FixTransactions;
202  use MoveAliases;  use MoveAliases;
203    
204  # Get the command-line options.  # Get the command-line options.
205  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,
206                                                        start => ' '},
207                                                    @ARGV);                                                    @ARGV);
208  # Get the command.  # Get the command.
209  my $mainCommand = lc shift @parameters;  my $mainCommand = lc shift @parameters;
# Line 213  Line 228 
228      $controlBlock = FixTransactions->new($options, $mainCommand, @parameters);      $controlBlock = FixTransactions->new($options, $mainCommand, @parameters);
229  } elsif ($mainCommand eq 'aliasmove') {  } elsif ($mainCommand eq 'aliasmove') {
230      $controlBlock = MoveAliases->new($options, $mainCommand, @parameters);      $controlBlock = MoveAliases->new($options, $mainCommand, @parameters);
231    } elsif ($mainCommand eq 'attribute') {
232        $controlBlock = AttributeTransactions->new($options, $mainCommand, @parameters);
233    } elsif ($mainCommand eq 'attributecheck') {
234        $controlBlock = AttributeTransactions->new($options, $mainCommand, @parameters);
235  } else {  } else {
236      Confess("Invalid command \"$mainCommand\" specified on command line.");      Confess("Invalid command \"$mainCommand\" specified on command line.");
237  }  }
# Line 227  Line 246 
246      my $orgsFound = 0;      my $orgsFound = 0;
247      my %transFiles = ();      my %transFiles = ();
248      my @transDirectory = OpenDir($parameters[0], 1);      my @transDirectory = OpenDir($parameters[0], 1);
249        # Pull out the "start" option value. This will be a space if all genomes should
250        # be processed, in which case it will always compare less than the genome ID.
251        my $startGenome = $options->{start};
252      # The next step is to create a hash of organism IDs to file names. This      # The next step is to create a hash of organism IDs to file names. This
253      # saves us some painful parsing later.      # saves us some painful parsing later.
254      for my $transFileName (@transDirectory) {      for my $transFileName (@transDirectory) {
255            # Parse the file name. This will only match if it's a real transaction file.
256          if ($transFileName =~ /^tbl_diff_(\d+\.\d+)$/) {          if ($transFileName =~ /^tbl_diff_(\d+\.\d+)$/) {
257                # Get the genome ID;
258                my $genomeID = $1;
259                # If we're skipping, only include this genome ID if it's equal to
260                # or greater than the start value.
261                if ($genomeID > $startGenome) {
262              $transFiles{$1} = "$parameters[0]/$transFileName";              $transFiles{$1} = "$parameters[0]/$transFileName";
263              $orgsFound++;              $orgsFound++;
264          }          }
265      }      }
266        }
267      Trace("$orgsFound genome transaction files found in directory $parameters[0].") if T(2);      Trace("$orgsFound genome transaction files found in directory $parameters[0].") if T(2);
268      if (! $orgsFound) {      if (! $orgsFound) {
269          Confess("No \"tbl_diff\" files found in directory $parameters[1].");          Confess("No \"tbl_diff\" files found in directory $parameters[1].");

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