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=head1 Load Sprout Tables |
=head1 Load Sprout Tables |
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Create the load files for a group of Sprout tables. The parameters are the names of |
=head2 Introduction |
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the table groups whose data is to be created. The legal table group names are given below. |
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This script creates the load files for Sprout tables and optionally loads them. |
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The parameters are the names of the table groups whose data is to be created. |
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The legal table group names are given below. |
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=over 4 |
=over 4 |
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=back |
=back |
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=head2 Usage |
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To load all the Sprout tables and then validate the result, you need to issue three |
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commands. |
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LoadSproutTables -dbLoad "*" |
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TestSproutLoad |
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index_sprout |
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All three commands send output to the console. In addition, C<LoadSproutTables> and |
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C<TestSproutLoad> write tracing information to C<trace.log> in the FIG temporary |
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directory (B<$FIG_Config::Tmp>). At the bottom of the log file will be a complete |
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list of errors. If errors occur in C<LoadSproutTables>, then the data must be corrected |
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and the offending table group reloaded. So, for example, if there are errors in the |
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load of the B<MadeAnnotation> and B<Compound> tables, you would need to run |
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LoadSproutTables -dbLoad Annotation Reaction |
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because B<MadeAnnotation> is in the C<Annotation> group, and B<Compound> is in the |
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C<Reaction> group. You can omit the C<dbLoad> option to create the load files without |
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loading the database, and you can add a C<trace> option to change the trace level. |
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The command below creates the Genome-related load files with a trace level of 3 and |
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does not load them into the Sprout database. |
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LoadSproutTables -trace=3 Genome |
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C<LoadSproutTables> takes a long time to run, so setting the trace level to 3 helps |
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to give you an idea of the progress. |
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Once the Sprout database is loaded, B<TestSproutLoad> can be used to verify the load |
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against the FIG data. Again, the end of the C<trace.log> file will contain a summary |
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of the errors found. Like C<LoadSproutTables>, C<TestSproutLoad> is a time-consuming |
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script, so you may want to set the trace level to 3 to see visible progress. |
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TestSproutLoad -trace=3 |
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Unlike C<LoadSproutTables>, in C<TestSproutLoad>, the individual errors found are |
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mixed in with the trace messages. They are all, however, marked with a trace type |
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of B<Problem>, as shown in the fragment below. |
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11/02/2005 19:15:16 <main>: Processing feature fig|100226.1.peg.7742. |
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11/02/2005 19:15:17 <main>: Processing feature fig|100226.1.peg.7741. |
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11/02/2005 19:15:17 <Problem>: assignment "Short-chain dehydrodenase ... |
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11/02/2005 19:15:17 <Problem>: assignment "putative oxidoreductase." ... |
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11/02/2005 19:15:17 <Problem>: Incorrect assignment for fig|100226.1.peg.7741... |
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11/02/2005 19:15:17 <Problem>: Incorrect number of annotations found in ... |
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11/02/2005 19:15:17 <main>: Processing feature fig|100226.1.peg.7740. |
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11/02/2005 19:15:18 <main>: Processing feature fig|100226.1.peg.7739. |
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The test may reveal that some tables need to be reloaded, or that a software |
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problem has crept into the Sprout. |
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Once all the tables have the correct data, C<index_sprout> can be run to create the |
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Glimpse indexes. |
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=cut |
=cut |
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use strict; |
use strict; |
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