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revision 1.15, Mon Sep 12 00:24:37 2005 UTC revision 1.20, Tue Feb 5 03:54:42 2008 UTC
# Line 1  Line 1 
1  #!/usr/bin/perl -w  #!/usr/bin/perl -w
2    #
3    # Copyright (c) 2003-2006 University of Chicago and Fellowship
4    # for Interpretations of Genomes. All Rights Reserved.
5    #
6    # This file is part of the SEED Toolkit.
7    #
8    # The SEED Toolkit is free software. You can redistribute
9    # it and/or modify it under the terms of the SEED Toolkit
10    # Public License.
11    #
12    # You should have received a copy of the SEED Toolkit Public License
13    # along with this program; if not write to the University of Chicago
14    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15    # Genomes at veronika@thefig.info or download a copy from
16    # http://www.theseed.org/LICENSE.TXT.
17    #
18    
19    
20  =head1 Add / Delete / Change Features  =head1 Add / Delete / Change Features
21    
# Line 168  Line 185 
185    
186  use strict;  use strict;
187  use Tracer;  use Tracer;
 use DocUtils;  
188  use Cwd;  use Cwd;
189  use File::Copy;  use File::Copy;
190  use File::Path;  use File::Path;
# Line 180  Line 196 
196  use FudgeTransactions;  use FudgeTransactions;
197    
198  # Get the command-line options.  # Get the command-line options.
199  my ($options, @parameters) = Tracer::ParseCommand({ trace => 3, sql => 0, safe => 0, noAlias => 0,  my ($options, @parameters) = StandardSetup(["FIG"],
200                                                      start => ' ', tblFiles => 0},                      { safe => [0, "use database transactions"],
201                          trace => [2, "trace level"],
202                          noAlias => [0, "do not expect aliases in CHANGE transactions"],
203                          start => [' ', "start with this genome"],
204                          tblFiles => [0, "output TBL files containing the corrected IDs"] },
205                        "command transactionDirectory IDfile",
206                                                    @ARGV);                                                    @ARGV);
207  # Get the command.  # Get the command.
208  my $mainCommand = lc shift @parameters;  my $mainCommand = lc shift @parameters;
 # Set up tracing.  
 my $traceLevel = $options->{trace};  
 my $tracing = "$traceLevel Tracer DocUtils FIG";  
 if ($options->{sql}) {  
     $tracing .= " SQL";  
 }  
 TSetup($tracing, "TEXT");  
209  # Get the FIG object.  # Get the FIG object.
210  my $fig = FIG->new();  my $fig = FIG->new();
211  # Create the transaction object.  # Create the transaction object.

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