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revision 1.14, Thu Sep 1 09:39:31 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 16  Line 33 
33  =item count  =item count
34    
35  Count the number of IDs needed to process the ADD and CHANGE transactions. This  Count the number of IDs needed to process the ADD and CHANGE transactions. This
36  will produce an listing of the number of feature IDs needed for each  will produce a listing of the number of feature IDs needed for each
37  organism and feature type. This command is mostly a sanity check: it provides  organism and feature type. This command is mostly a sanity check: it provides
38  useful statistics without changing anything.  useful statistics without changing anything.
39    
# Line 153  Line 170 
170    
171  Trace SQL commands.  Trace SQL commands.
172    
173    =item tblFiles
174    
175    Output TBL files containing the corrected IDs. (B<process> command only)
176    
177  =item start  =item start
178    
179  ID of the first genome to process. This allows restarting a transaction run that failed  ID of the first genome to process. This allows restarting a transaction run that failed
# Line 164  Line 185 
185    
186  use strict;  use strict;
187  use Tracer;  use Tracer;
 use DocUtils;  
 use TestUtils;  
188  use Cwd;  use Cwd;
189  use File::Copy;  use File::Copy;
190  use File::Path;  use File::Path;
# Line 177  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 => ' '},                      { 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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