View of /Sprout/LoadSproutTables.pl

#!/usr/bin/perl -w

=head1 Load Sprout Tables

Create the load files for a group of Sprout tables. The parameters are the names of
the table groups whose data is to be created. The legal table group names are given below.

=over 4

=item Genome

Loads B<Genome>, B<HasContig>, B<Contig>, B<IsMadeUpOf>, and B<Sequence>.

=item Coupling

Loads B<Coupling>, B<IsEvidencedBy>, B<PCH>, B<ParticipatesInCoupling>,
B<UsesAsEvidence>.

=item Feature

Loads B<Feature>, B<FeatureAlias>, B<FeatureTranslation>, B<FeatureUpstream>,
B<IsLocatedIn>, B<FeatureLink>.

=item Subsystem

Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,
B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>,
B<Catalyzes>, B<Reaction>, B<ConsistsOfRoles>, B<RoleSubset>, B<HasRoleSubset>,
B<ConsistsOfGenomes>, B<GenomeSubset>, B<HasGenomeSubset>

=item Annotation

Loads B<SproutUser>, B<UserAccess>, B<Annotation>, B<IsTargetOfAnnotation>,
B<MadeAnnotation>.

=item Diagram

Loads B<Diagram>, B<RoleOccursIn>.

=item Property

Loads B<Property>, B<HasProperty>.

=item BBH

Loads B<IsBidirectionalBestHitOf>.

=item Group

Loads B<GenomeGroups>.

=item Source

Loads B<Source>, B<ComesFrom>, B<SourceURL>.

=item External

Loads B<ExternalAliasOrg>, B<ExternalAliasFunc>.

=item Reaction

Loads B<ReactionURL>, B<Compound>, B<CompoundName>,
B<CompoundCAS>, B<IsAComponentOf>.

=item *

Loads all of the above tables.

=back

The command-line options are given below.

=over 4

=item geneFile

The name of the file containing the genomes and their associated access codes. The
file should have one line per genome, each line consisting of the genome ID followed
by the access code, separated by a tab. If no file is specified, all complete genomes
will be processed and the access code will be 1.

=item subsysFile

The name of the file containing the trusted subsystems. The file should have one line
per trusted subsystem. If no file is specified, all subsystems will be trusted.

=item trace

Desired tracing level. The default is 3.

=item limitedFeatures

Only generate the B<Feature> and B<IsLocatedIn> tables when processing the feature group.

=item dbLoad

If TRUE, the database tables will be loaded automatically from the load files created.

=back

=cut

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

# Get the command-line parameters and options.
my ($options, @parameters) = Tracer::ParseCommand({ geneFile => "", subsysFile => "",
                                                    trace => 3, limitedFeatures => 0,
                                                    dbLoad => 0 }, @ARGV);
# Set up tracing.
TSetup("$options->{trace} SproutLoad ERDBLoad ERDB Stats Tracer Load", "+>$FIG_Config::temp/trace.log");
# Create the sprout loader object. Note that the Sprout object does not
# open the database unless the "dbLoad" option is turned on.
my $fig = FIG->new();
my $sprout = SFXlate->new_sprout_only(undef, undef, undef, ! $options->{dbLoad});
my $spl = SproutLoad->new($sprout, $fig, $options->{geneFile}, $options->{subsysFile}, $options);
# Process the parameters.
for my $group (@parameters) {
    Trace("Processing load group $group.") if T(2);
    my $stats;
    if ($group eq 'Genome' || $group eq '*') {
        $spl->LoadGenomeData();
    }
    if ($group eq 'Feature' || $group eq '*') {
        $spl->LoadFeatureData();
    }
    if ($group eq 'Coupling' || $group eq '*') {
        $spl->LoadCouplingData();
    }
    if ($group eq 'Subsystem' || $group eq '*') {
        $spl->LoadSubsystemData();
    }
    if ($group eq 'Property' || $group eq '*') {
        $spl->LoadPropertyData();
    }
    if ($group eq 'Diagram' || $group eq '*') {
        $spl->LoadDiagramData();
    }
    if ($group eq 'Annotation' || $group eq '*') {
        $spl->LoadAnnotationData();
    }
    if ($group eq 'BBH' || $group eq '*') {
        $spl->LoadBBHData();
    }
    if ($group eq 'Group' || $group eq '*') {
        $spl->LoadGroupData();
    }
    if ($group eq 'Source' || $group eq '*') {
        $spl->LoadSourceData();
    }
    if ($group eq 'External' || $group eq '*') {
        $spl->LoadExternalData();
    }
    if ($group eq 'Reaction' || $group eq '*') {
        $spl->LoadReactionData();
    }

}
Trace("Load complete.") if T(2);

1;