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revision 1.6, Sun May 16 22:50:17 2010 UTC revision 1.14, Tue Jun 15 19:08:48 2010 UTC
# Line 24  Line 24 
24  (-s "$orgD/Features/peg/tbl")  (-s "$orgD/Features/peg/tbl")
25      || die "Where is $orgD/Features/peg/tbl?";      || die "Where is $orgD/Features/peg/tbl?";
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");  my $tbl = (-s "$exp_ed/tbl") ? "$exp_ed/tbl" : "$orgD/Features/peg/tbl";
28    &run("make_probes_to_genes $exp_ed/probes $orgD/contigs $tbl $exp_ed/peg.probe.table $exp_ed/probe.occ.table 2> $exp_ed/problems");
29  &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";  
30  chdir $exp_ed;  chdir $exp_ed;
31    
32  &run("Rscript $FIG_Config::bin/RunRMA.R $rma_key $exp_ed/peg.probe.table $exp_ed/Experiments 2> $exp_ed/stderr.RMA");  my $peg_probe_table = "$exp_ed/peg.probe.table.no.multiple";
33    my $probe_no_match = "$exp_ed/probe.no.match";
34    
35    &make_missing_probes($peg_probe_table, "$exp_ed/probes", $probe_no_match);
36    
37    &run("Rscript $FIG_Config::bin/RunRMA.R $peg_probe_table $probe_no_match $exp_ed/Experiments $exp_ed 2> $exp_ed/stderr.RMA");
38    
39    #&run("Rscript $FIG_Config::bin/RunRMA.R $rma_key $exp_ed $exp_ed/Experiments 2> $exp_ed/stderr.RMA");
40    
41  &run("$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> $exp_ed/stderr.coregulated.clusters");
42  &run("$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");
43  &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");
44    
45  &run("get_ON_probes $genome $exp_ed/probe.occ.table $exp_ed/peg.probe.table > $exp_ed/pegs.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");
46    &run("cut -f2 $exp_ed/probes.always.on | sort -u > $exp_ed/pegs.always.on");
47  &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");
48    
49  &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 > $exp_ed/split.clusters");
50  system "popd";  
51    sub make_missing_probes
52    {
53        my($probe_table, $probes, $output) = @_;
54        open(MATCH,"<", $probe_table) or die "Cannot open $probe_table: $!";
55        open(PROBES,"<", $probes) or die "Cannot open $probes: $!";
56        open(OUTPUT, ">", $output) or die "Cannot open $output: $!";
57        my %locations;
58        while(<MATCH>)
59        {
60            chomp;
61            my($peg,$loc)=split "\t";
62            $locations{$loc} = $peg;
63        }
64    
65        while(<PROBES>)
66        {
67            chomp;
68            my($loc,$seq) = split "\t";
69            print OUTPUT $loc, "\n" if ! exists $locations{$loc};
70        }
71        close(MATCH);
72        close(PROBES);
73        close(OUTPUT);
74    }
75    
76  sub run {  sub run {
77      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);

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