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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 :     B<Catalyzes>, B<Reaction>, B<ConsistsOfRoles>, B<RoleSubset>, B<HasRoleSubset>,
29 :     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 :     B<CompoundCAS>, B<IsAComponentOf>.
64 :    
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 1.1 =back
96 :    
97 :     =cut
98 :    
99 :     use strict;
100 :     use Tracer;
101 :     use DocUtils;
102 :     use Cwd;
103 :     use FIG;
104 :     use SFXlate;
105 :     use File::Copy;
106 :     use File::Path;
107 :     use SproutLoad;
108 :     use Stats;
109 :    
110 :     # Get the command-line parameters and options.
111 :     my ($options, @parameters) = Tracer::ParseCommand({ geneFile => "", subsysFile => "",
112 : parrello 1.7 trace => 3, limitedFeatures => 0 },
113 : parrello 1.1 @ARGV);
114 :     # Set up tracing.
115 : parrello 1.4 TSetup("$options->{trace} SproutLoad ERDBLoad ERDB Stats Tracer Load", "+>$FIG_Config::temp/trace.log");
116 : parrello 1.1 # Create the sprout loader object.
117 :     my $fig = FIG->new();
118 : parrello 1.6 my $sprout = Sprout->new($FIG_Config::sproutDB, { noDBOpen => 1 });
119 : parrello 1.7 my $spl = SproutLoad->new($sprout, $fig, $options->{geneFile}, $options->{subsysFile}, $options);
120 : parrello 1.1 # Process the parameters.
121 :     for my $group (@parameters) {
122 :     Trace("Processing load group $group.") if T(2);
123 :     my $stats;
124 : parrello 1.3 if ($group eq 'Genome' || $group eq '*') {
125 : parrello 1.1 $spl->LoadGenomeData();
126 : parrello 1.3 }
127 :     if ($group eq 'Feature' || $group eq '*') {
128 : parrello 1.1 $spl->LoadFeatureData();
129 : parrello 1.3 }
130 :     if ($group eq 'Coupling' || $group eq '*') {
131 : parrello 1.1 $spl->LoadCouplingData();
132 : parrello 1.3 }
133 :     if ($group eq 'Subsystem' || $group eq '*') {
134 : parrello 1.1 $spl->LoadSubsystemData();
135 : parrello 1.3 }
136 :     if ($group eq 'Property' || $group eq '*') {
137 : parrello 1.1 $spl->LoadPropertyData();
138 : parrello 1.3 }
139 :     if ($group eq 'Diagram' || $group eq '*') {
140 : parrello 1.2 $spl->LoadDiagramData();
141 : parrello 1.3 }
142 :     if ($group eq 'Annotation' || $group eq '*') {
143 : parrello 1.2 $spl->LoadAnnotationData();
144 : parrello 1.3 }
145 :     if ($group eq 'BBH' || $group eq '*') {
146 : parrello 1.2 $spl->LoadBBHData();
147 : parrello 1.1 }
148 : parrello 1.4 if ($group eq 'Group' || $group eq '*') {
149 : parrello 1.3 $spl->LoadGroupData();
150 :     }
151 :     if ($group eq 'Source' || $group eq '*') {
152 :     $spl->LoadSourceData();
153 :     }
154 : parrello 1.4 if ($group eq 'External' || $group eq '*') {
155 :     $spl->LoadExternalData();
156 :     }
157 : parrello 1.8 if ($group eq 'Reaction' || $group eq '*') {
158 :     $spl->LoadReactionData();
159 :     }
160 : parrello 1.3
161 : parrello 1.1 }
162 :     Trace("Load complete.") if T(2);
163 :    
164 :     1;

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