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| 1 : | parrello | 1.1 | #!/usr/bin/perl -w |
| 2 : | |||
| 3 : | =head1 Load Sprout Tables | ||
| 4 : | |||
| 5 : | parrello | 1.3 | Create the load files for a group of Sprout tables. The parameters are the names of |
| 6 : | the table groups whose data is to be created. The legal table group names are given below. | ||
| 7 : | parrello | 1.1 | |
| 8 : | =over 4 | ||
| 9 : | |||
| 10 : | =item Genome | ||
| 11 : | |||
| 12 : | Loads B<Genome>, B<HasContig>, B<Contig>, B<IsMadeUpOf>, and B<Sequence>. | ||
| 13 : | |||
| 14 : | =item Coupling | ||
| 15 : | |||
| 16 : | Loads B<Coupling>, B<IsEvidencedBy>, B<PCH>, B<ParticipatesInCoupling>, | ||
| 17 : | B<UsesAsEvidence>. | ||
| 18 : | |||
| 19 : | =item Feature | ||
| 20 : | |||
| 21 : | Loads B<Feature>, B<FeatureAlias>, B<FeatureTranslation>, B<FeatureUpstream>, | ||
| 22 : | parrello | 1.2 | B<IsLocatedIn>, B<FeatureLink>. |
| 23 : | parrello | 1.1 | |
| 24 : | =item Subsystem | ||
| 25 : | |||
| 26 : | parrello | 1.2 | Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>, |
| 27 : | parrello | 1.8 | B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>, |
| 28 : | parrello | 1.11 | B<Catalyzes>, B<ConsistsOfRoles>, B<RoleSubset>, B<HasRoleSubset>, |
| 29 : | parrello | 1.8 | B<ConsistsOfGenomes>, B<GenomeSubset>, B<HasGenomeSubset> |
| 30 : | parrello | 1.1 | |
| 31 : | parrello | 1.2 | =item Annotation |
| 32 : | |||
| 33 : | Loads B<SproutUser>, B<UserAccess>, B<Annotation>, B<IsTargetOfAnnotation>, | ||
| 34 : | B<MadeAnnotation>. | ||
| 35 : | |||
| 36 : | =item Diagram | ||
| 37 : | |||
| 38 : | Loads B<Diagram>, B<RoleOccursIn>. | ||
| 39 : | |||
| 40 : | =item Property | ||
| 41 : | |||
| 42 : | Loads B<Property>, B<HasProperty>. | ||
| 43 : | |||
| 44 : | =item BBH | ||
| 45 : | |||
| 46 : | Loads B<IsBidirectionalBestHitOf>. | ||
| 47 : | |||
| 48 : | parrello | 1.3 | =item Group |
| 49 : | |||
| 50 : | Loads B<GenomeGroups>. | ||
| 51 : | |||
| 52 : | =item Source | ||
| 53 : | |||
| 54 : | Loads B<Source>, B<ComesFrom>, B<SourceURL>. | ||
| 55 : | |||
| 56 : | parrello | 1.4 | =item External |
| 57 : | |||
| 58 : | Loads B<ExternalAliasOrg>, B<ExternalAliasFunc>. | ||
| 59 : | |||
| 60 : | parrello | 1.8 | =item Reaction |
| 61 : | |||
| 62 : | Loads B<ReactionURL>, B<Compound>, B<CompoundName>, | ||
| 63 : | parrello | 1.11 | B<CompoundCAS>, B<IsAComponentOf>, B<Reaction>. |
| 64 : | parrello | 1.8 | |
| 65 : | parrello | 1.3 | =item * |
| 66 : | |||
| 67 : | Loads all of the above tables. | ||
| 68 : | |||
| 69 : | parrello | 1.1 | =back |
| 70 : | |||
| 71 : | parrello | 1.7 | The command-line options are given below. |
| 72 : | parrello | 1.1 | |
| 73 : | =over 4 | ||
| 74 : | |||
| 75 : | =item geneFile | ||
| 76 : | |||
| 77 : | The name of the file containing the genomes and their associated access codes. The | ||
| 78 : | file should have one line per genome, each line consisting of the genome ID followed | ||
| 79 : | by the access code, separated by a tab. If no file is specified, all complete genomes | ||
| 80 : | will be processed and the access code will be 1. | ||
| 81 : | |||
| 82 : | =item subsysFile | ||
| 83 : | |||
| 84 : | The name of the file containing the trusted subsystems. The file should have one line | ||
| 85 : | per trusted subsystem. If no file is specified, all subsystems will be trusted. | ||
| 86 : | |||
| 87 : | =item trace | ||
| 88 : | |||
| 89 : | Desired tracing level. The default is 3. | ||
| 90 : | |||
| 91 : | parrello | 1.7 | =item limitedFeatures |
| 92 : | |||
| 93 : | Only generate the B<Feature> and B<IsLocatedIn> tables when processing the feature group. | ||
| 94 : | |||
| 95 : | parrello | 1.10 | =item dbLoad |
| 96 : | |||
| 97 : | If TRUE, the database tables will be loaded automatically from the load files created. | ||
| 98 : | |||
| 99 : | parrello | 1.1 | =back |
| 100 : | |||
| 101 : | =cut | ||
| 102 : | |||
| 103 : | use strict; | ||
| 104 : | use Tracer; | ||
| 105 : | use DocUtils; | ||
| 106 : | use Cwd; | ||
| 107 : | use FIG; | ||
| 108 : | use SFXlate; | ||
| 109 : | use File::Copy; | ||
| 110 : | use File::Path; | ||
| 111 : | use SproutLoad; | ||
| 112 : | use Stats; | ||
| 113 : | parrello | 1.9 | use SFXlate; |
| 114 : | parrello | 1.1 | |
| 115 : | # Get the command-line parameters and options. | ||
| 116 : | my ($options, @parameters) = Tracer::ParseCommand({ geneFile => "", subsysFile => "", | ||
| 117 : | parrello | 1.10 | trace => 3, limitedFeatures => 0, |
| 118 : | dbLoad => 0 }, @ARGV); | ||
| 119 : | parrello | 1.1 | # Set up tracing. |
| 120 : | parrello | 1.4 | TSetup("$options->{trace} SproutLoad ERDBLoad ERDB Stats Tracer Load", "+>$FIG_Config::temp/trace.log"); |
| 121 : | parrello | 1.9 | # Create the sprout loader object. Note that the Sprout object does not |
| 122 : | parrello | 1.10 | # open the database unless the "dbLoad" option is turned on. |
| 123 : | parrello | 1.1 | my $fig = FIG->new(); |
| 124 : | parrello | 1.10 | my $sprout = SFXlate->new_sprout_only(undef, undef, undef, ! $options->{dbLoad}); |
| 125 : | parrello | 1.7 | my $spl = SproutLoad->new($sprout, $fig, $options->{geneFile}, $options->{subsysFile}, $options); |
| 126 : | parrello | 1.1 | # Process the parameters. |
| 127 : | for my $group (@parameters) { | ||
| 128 : | Trace("Processing load group $group.") if T(2); | ||
| 129 : | my $stats; | ||
| 130 : | parrello | 1.3 | if ($group eq 'Genome' || $group eq '*') { |
| 131 : | parrello | 1.1 | $spl->LoadGenomeData(); |
| 132 : | parrello | 1.3 | } |
| 133 : | if ($group eq 'Feature' || $group eq '*') { | ||
| 134 : | parrello | 1.1 | $spl->LoadFeatureData(); |
| 135 : | parrello | 1.3 | } |
| 136 : | if ($group eq 'Coupling' || $group eq '*') { | ||
| 137 : | parrello | 1.1 | $spl->LoadCouplingData(); |
| 138 : | parrello | 1.3 | } |
| 139 : | if ($group eq 'Subsystem' || $group eq '*') { | ||
| 140 : | parrello | 1.1 | $spl->LoadSubsystemData(); |
| 141 : | parrello | 1.3 | } |
| 142 : | if ($group eq 'Property' || $group eq '*') { | ||
| 143 : | parrello | 1.1 | $spl->LoadPropertyData(); |
| 144 : | parrello | 1.3 | } |
| 145 : | if ($group eq 'Diagram' || $group eq '*') { | ||
| 146 : | parrello | 1.2 | $spl->LoadDiagramData(); |
| 147 : | parrello | 1.3 | } |
| 148 : | if ($group eq 'Annotation' || $group eq '*') { | ||
| 149 : | parrello | 1.2 | $spl->LoadAnnotationData(); |
| 150 : | parrello | 1.3 | } |
| 151 : | if ($group eq 'BBH' || $group eq '*') { | ||
| 152 : | parrello | 1.2 | $spl->LoadBBHData(); |
| 153 : | parrello | 1.1 | } |
| 154 : | parrello | 1.4 | if ($group eq 'Group' || $group eq '*') { |
| 155 : | parrello | 1.3 | $spl->LoadGroupData(); |
| 156 : | } | ||
| 157 : | if ($group eq 'Source' || $group eq '*') { | ||
| 158 : | $spl->LoadSourceData(); | ||
| 159 : | } | ||
| 160 : | parrello | 1.4 | if ($group eq 'External' || $group eq '*') { |
| 161 : | $spl->LoadExternalData(); | ||
| 162 : | } | ||
| 163 : | parrello | 1.8 | if ($group eq 'Reaction' || $group eq '*') { |
| 164 : | $spl->LoadReactionData(); | ||
| 165 : | } | ||
| 166 : | parrello | 1.3 | |
| 167 : | parrello | 1.1 | } |
| 168 : | Trace("Load complete.") if T(2); | ||
| 169 : | |||
| 170 : | 1; |
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