[Bio] / Sprout / LoadSproutTables.pl Repository:
ViewVC logotype

Diff of /Sprout/LoadSproutTables.pl

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.11, Wed Nov 2 21:45:08 2005 UTC revision 1.12, Mon Nov 7 20:29:46 2005 UTC
# Line 2  Line 2 
2    
3  =head1 Load Sprout Tables  =head1 Load Sprout Tables
4    
5  Create the load files for a group of Sprout tables. The parameters are the names of  =head2 Introduction
6  the table groups whose data is to be created. The legal table group names are given below.  
7    This script creates the load files for Sprout tables and optionally loads them.
8    The parameters are the names of the table groups whose data is to be created.
9    The legal table group names are given below.
10    
11  =over 4  =over 4
12    
# Line 98  Line 101 
101    
102  =back  =back
103    
104    =head2 Usage
105    
106    To load all the Sprout tables and then validate the result, you need to issue three
107    commands.
108    
109        LoadSproutTables -dbLoad "*"
110        TestSproutLoad
111        index_sprout
112    
113    All three commands send output to the console. In addition, C<LoadSproutTables> and
114    C<TestSproutLoad> write tracing information to C<trace.log> in the FIG temporary
115    directory (B<$FIG_Config::Tmp>). At the bottom of the log file will be a complete
116    list of errors. If errors occur in C<LoadSproutTables>, then the data must be corrected
117    and the offending table group reloaded. So, for example, if there are errors in the
118    load of the B<MadeAnnotation> and B<Compound> tables, you would need to run
119    
120        LoadSproutTables -dbLoad Annotation Reaction
121    
122    because B<MadeAnnotation> is in the C<Annotation> group, and B<Compound> is in the
123    C<Reaction> group. You can omit the C<dbLoad> option to create the load files without
124    loading the database, and you can add a C<trace> option to change the trace level.
125    The command below creates the Genome-related load files with a trace level of 3 and
126    does not load them into the Sprout database.
127    
128        LoadSproutTables -trace=3 Genome
129    
130    C<LoadSproutTables> takes a long time to run, so setting the trace level to 3 helps
131    to give you an idea of the progress.
132    
133    Once the Sprout database is loaded, B<TestSproutLoad> can be used to verify the load
134    against the FIG data. Again, the end of the C<trace.log> file will contain a summary
135    of the errors found. Like C<LoadSproutTables>, C<TestSproutLoad> is a time-consuming
136    script, so you may want to set the trace level to 3 to see visible progress.
137    
138        TestSproutLoad -trace=3
139    
140    Unlike C<LoadSproutTables>, in C<TestSproutLoad>, the individual errors found are
141    mixed in with the trace messages. They are all, however, marked with a trace type
142    of B<Problem>, as shown in the fragment below.
143    
144        11/02/2005 19:15:16 <main>: Processing feature fig|100226.1.peg.7742.
145        11/02/2005 19:15:17 <main>: Processing feature fig|100226.1.peg.7741.
146        11/02/2005 19:15:17 <Problem>: assignment "Short-chain dehydrodenase ...
147        11/02/2005 19:15:17 <Problem>: assignment "putative oxidoreductase." ...
148        11/02/2005 19:15:17 <Problem>: Incorrect assignment for fig|100226.1.peg.7741...
149        11/02/2005 19:15:17 <Problem>: Incorrect number of annotations found in ...
150        11/02/2005 19:15:17 <main>: Processing feature fig|100226.1.peg.7740.
151        11/02/2005 19:15:18 <main>: Processing feature fig|100226.1.peg.7739.
152    
153    The test may reveal that some tables need to be reloaded, or that a software
154    problem has crept into the Sprout.
155    
156    Once all the tables have the correct data, C<index_sprout> can be run to create the
157    Glimpse indexes.
158    
159  =cut  =cut
160    
161  use strict;  use strict;

Legend:
Removed from v.1.11  
changed lines
  Added in v.1.12

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3