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revision 1.5, Sun May 16 00:38:02 2010 UTC revision 1.8, Mon May 17 13:30:58 2010 UTC
# Line 32  Line 32 
32  &run("Rscript $FIG_Config::bin/RunRMA.R $rma_key $exp_ed/peg.probe.table $exp_ed/Experiments 2> $exp_ed/stderr.RMA");  &run("Rscript $FIG_Config::bin/RunRMA.R $rma_key $exp_ed/peg.probe.table $exp_ed/Experiments 2> $exp_ed/stderr.RMA");
33  &run("$FIG_Config::bin/call_coregulated_clusters_on_chromosome $genome $exp_ed/raw_data.tab > $exp_ed/coregulated.clusters 2> $exp_ed/stderr.coregulated.clusters");  &run("$FIG_Config::bin/call_coregulated_clusters_on_chromosome $genome $exp_ed/raw_data.tab > $exp_ed/coregulated.clusters 2> $exp_ed/stderr.coregulated.clusters");
34  &run("$FIG_Config::bin/make_coreg_conjectures_based_on_subsys  $genome $exp_ed/raw_data.tab > $exp_ed/coregulated.subsys   2> $exp_ed/stderr.coregulated.subsys");  &run("$FIG_Config::bin/make_coreg_conjectures_based_on_subsys  $genome $exp_ed/raw_data.tab > $exp_ed/coregulated.subsys   2> $exp_ed/stderr.coregulated.subsys");
35  &run("cat $exp_ed/coregulated.clusters $exp_ed/coregulated.subsys | cut -f1 | $FIG_Config::bin/merge_gene_sets | filter_on_known > $exp_ed/merged.clusters");  &run("cat $exp_ed/coregulated.clusters $exp_ed/coregulated.subsys | cut -f1 | $FIG_Config::bin/merge_gene_sets | filter_on_known $exp_ed/raw_data.tab > $exp_ed/merged.clusters");
36    
37  &run("get_ON_probes $genome $exp_ed/probe.occ.table $exp_ed/peg.probe.table > $exp_ed/probes.always.on");  &run("get_ON_probes $genome $exp_ed/probe.occ.table $exp_ed/peg.probe.table $exp_ed/raw_data.tab > $exp_ed/probes.always.on");
38  &run("Rscript $FIG_Config::bin/Pipeline.R $exp_ed/probes.always.on $exp_ed/merged.clusters > $exp_ed/comments.by.Pipeline.R");  &run("cut -f2 $exp_ed/probes.always.on | sort -u > $exp_ed/pegs.always.on");
39    &run("Rscript $FIG_Config::bin/Pipeline.R $exp_ed/pegs.always.on $exp_ed/merged.clusters > $exp_ed/comments.by.Pipeline.R");
40  &run("Rscript $FIG_Config::bin/SplitGeneSets.R $exp_ed/merged.clusters 0.7 > $exp_ed/split.clusters");  &run("Rscript $FIG_Config::bin/SplitGeneSets.R $exp_ed/merged.clusters 0.7 > $exp_ed/split.clusters");
41  system "popd";  system "popd";
42    

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