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Revision 1.3 - (download) (as text) (annotate)
Tue Apr 14 00:07:03 2009 UTC (10 years, 7 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, mgrast_dev_05262011, mgrast_dev_04082011, rast_rel_2010_0928, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, rast_rel_2011_0119, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, mgrast_dev_04012011, rast_rel_2009_07_09, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_02222011, mgrast_dev_10262011, HEAD
Changes since 1.2: +1 -1 lines
fix first arg on call to mark_picked_genes

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 $dir/genomes $dir/ScoredAlignments $dir/Picked $dir/HTML");
&FIG::run("generate_comparisons $dir/genomes ../HTML $dir/Picked $dir/Comparisons");

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