[Bio] View of /Sprout/DeleteGenomes.pl

Revision 1.3 - (download) (as text) (annotate)
Tue Feb 5 05:47:32 2008 UTC (11 years, 10 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, rast_rel_2008_06_18, rast_rel_2008_06_16, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2009_05_18, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07
Changes since 1.2: +0 -2 lines

Removed obsolete use clauses.

#!/usr/bin/perl -w

=head1 Delete Genomes from Sprout

This method deletes genomes from the Sprout database. Simply list the genomes
as command-line parameters.

The currently-supported command-line options are as follows.

=over 4

=item showOnly

If specified, the DELETE statements will be displayed but no records will be deleted.

=item trace

Numeric trace level. A higher trace level causes more messages to appear. The
default trace level is 2.

=item sql

If specified, turns on tracing of SQL activity.

=item h

Display this commands parameters and options.

=back

=cut

use strict;
use Tracer;
use Cwd;
use FIG;
use Stats;
use Sprout;
use SFXlate;
use File::Copy;
use File::Path;

# Get the command-line options.
my ($options, @parameters) = StandardSetup(['ERDB', 'Sprout'],
                                        {
                                            showOnly => [0, 'Display DELETE statements without deleting.'],
                                            trace => [2, 'tracing level'],
                                        },
                                            '<genome1> <genome2> ...',
                                            @ARGV);
# Get the Sprout object.
my $sprout = SFXlate->new_sprout_only();
# Save the show-only flag.
my $showOnly = $options->{showOnly};
# Create the statistics object.
my $retVal = Stats->new('genomesFound', 'genomesNotFound');
# Loop through the genome IDs.
for my $genomeID (@parameters) {
    # Find out if the genome is real.
    if (! $sprout->Exists('Genome', $genomeID)) {
        # Warn the user. Nothing can get deleted if the genome is not in the Genome
        # table.
        Trace("Genome $genomeID not found in the genome table.") if T(1);
        $retVal->Add('genomesNotFound');
    } else {
        # Here we can delete it.
        my $stats = $sprout->DeleteGenome($genomeID, $showOnly);
        # Update the statistics.
        $retVal->Add('genomesFound');
        $retVal->Accumulate($stats);
    }
}
# Display the statistcs.
Trace($retVal->Show()) if T(0);

1;