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revision 1.8, Mon May 17 13:30:58 2010 UTC revision 1.9, Thu May 20 20:22:28 2010 UTC
# Line 26  Line 26 
26    
27  &run("make_probes_to_genes $exp_ed/probes $orgD/contigs $orgD/Features/peg/tbl $exp_ed/peg.probe.table $exp_ed/probe.occ.table 2> $exp_ed/problems");  &run("make_probes_to_genes $exp_ed/probes $orgD/contigs $orgD/Features/peg/tbl $exp_ed/peg.probe.table $exp_ed/probe.occ.table 2> $exp_ed/problems");
28  &run("remove_multiple_occurring_probes $exp_ed/peg.probe.table $exp_ed/probe.occ.table > $exp_ed/peg.probe.table.no.multiple");  &run("remove_multiple_occurring_probes $exp_ed/peg.probe.table $exp_ed/probe.occ.table > $exp_ed/peg.probe.table.no.multiple");
 system "pushd $exp_ed";  
29  chdir $exp_ed;  chdir $exp_ed;
30    
31  &run("Rscript $FIG_Config::bin/RunRMA.R $rma_key $exp_ed/peg.probe.table $exp_ed/Experiments 2> $exp_ed/stderr.RMA");  &make_missing_probes("$exp_ed/peg.probe.table.no.multiple", "$exp_ed/probes", "$exp_ed/probe.no.match");
32    
33    &run("Rscript $FIG_Config::bin/RunRMA.R $rma_key $exp_ed $exp_ed/Experiments 2> $exp_ed/stderr.RMA");
34  &run("$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> $exp_ed/stderr.coregulated.clusters");
35  &run("$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");
36  &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");  &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");
# Line 38  Line 39 
39  &run("cut -f2 $exp_ed/probes.always.on | sort -u > $exp_ed/pegs.always.on");  &run("cut -f2 $exp_ed/probes.always.on | sort -u > $exp_ed/pegs.always.on");
40  &run("Rscript $FIG_Config::bin/Pipeline.R $exp_ed/pegs.always.on $exp_ed/merged.clusters > $exp_ed/comments.by.Pipeline.R");  &run("Rscript $FIG_Config::bin/Pipeline.R $exp_ed/pegs.always.on $exp_ed/merged.clusters > $exp_ed/comments.by.Pipeline.R");
41  &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 > $exp_ed/split.clusters");
42  system "popd";  
43    sub make_missing_probes
44    {
45        my($probe_table, $probes, $output) = @_;
46        open(MATCH,"<", $probe_table) or die "Cannot open $probe_table: $!";
47        open(PROBES,"<", $probes) or die "Cannot open $probes: $!";
48        open(OUTPUT, ">", $output) or die "Cannot open $output: $!";
49        my %locations;
50        while(<MATCH>)
51        {
52            chomp;
53            my($peg,$loc)=split "\t";
54            $locations{$loc} = $peg;
55        }
56    
57        while(<PROBES>)
58        {
59            chomp;
60            my($loc,$seq) = split "\t";
61            print OUTPUT $loc, "\n" if ! exists $locations{$loc};
62        }
63        close(MATCH);
64        close(PROBES);
65        close(OUTPUT);
66    }
67    
68  sub run {  sub run {
69      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
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