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Revision 1.2 - (download) (as text) (annotate)
Mon Apr 13 14:35:06 2009 UTC (10 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.1: +1 -1 lines
fix parms - add contigs

use strict;
use FIG;

my $usage = "usage: run_gene_calling_scripts Dir-containing-genomes-file";
my $dir;

(
 ($dir = shift @ARGV) && (-d $dir) && (-s "$dir/genomes")
)
    || die $usage;

# The genomes file contains lines pf the form    GenomeId\tAbsolutePathToGenomeDirectory

if (-d "$dir/Instances")            { system "rm -r $dir/Instances" }
if (-d "$dir/ScoredAlignments")     { system "rm -r $dir/ScoredAlignments" }
if (-d "$dir/HTML")                 { system "rm -r $dir/HTML" }
if (-d "$dir/Picked")               { system "rm -r $dir/Picked" }
if (-d "$dir/Comparisons")          { system "rm -r $dir/Comparisons" }
&FIG::run("make_scored_instances $dir/genomes $dir/Instances $dir/ScoredAlignments $dir/contigs $dir/HTML");
&FIG::run("get_rna_features_for_calling_genes $dir/genomes $dir/Instances");
&FIG::run("generate_picked $dir/Instances $dir/Picked");
&FIG::run("mark_picked_genes genomes $dir/ScoredAlignments $dir/Picked $dir/HTML");
&FIG::run("generate_comparisons $dir/genomes ../HTML $dir/Picked $dir/Comparisons");

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