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Annotation of /FigKernelScripts/run_gene_calling_scripts.pl

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1 : overbeek 1.1 use strict;
2 :     use FIG;
3 :    
4 :     my $usage = "usage: run_gene_calling_scripts Dir-containing-genomes-file";
5 :     my $dir;
6 :    
7 :     (
8 :     ($dir = shift @ARGV) && (-d $dir) && (-s "$dir/genomes")
9 :     )
10 :     || die $usage;
11 :    
12 :     # The genomes file contains lines pf the form GenomeId\tAbsolutePathToGenomeDirectory
13 :    
14 :     if (-d "$dir/Instances") { system "rm -r $dir/Instances" }
15 :     if (-d "$dir/ScoredAlignments") { system "rm -r $dir/ScoredAlignments" }
16 :     if (-d "$dir/HTML") { system "rm -r $dir/HTML" }
17 :     if (-d "$dir/Picked") { system "rm -r $dir/Picked" }
18 :     if (-d "$dir/Comparisons") { system "rm -r $dir/Comparisons" }
19 : overbeek 1.2 &FIG::run("make_scored_instances $dir/genomes $dir/Instances $dir/ScoredAlignments $dir/contigs $dir/HTML");
20 : overbeek 1.1 &FIG::run("get_rna_features_for_calling_genes $dir/genomes $dir/Instances");
21 :     &FIG::run("generate_picked $dir/Instances $dir/Picked");
22 :     &FIG::run("mark_picked_genes genomes $dir/ScoredAlignments $dir/Picked $dir/HTML");
23 :     &FIG::run("generate_comparisons $dir/genomes ../HTML $dir/Picked $dir/Comparisons");

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