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revision 1.9, Thu May 20 20:22:28 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");
30  chdir $exp_ed;  chdir $exp_ed;
31    
32  &make_missing_probes("$exp_ed/peg.probe.table.no.multiple", "$exp_ed/probes", "$exp_ed/probe.no.match");  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    
 &run("Rscript $FIG_Config::bin/RunRMA.R $rma_key $exp_ed $exp_ed/Experiments 2> $exp_ed/stderr.RMA");  
41  &run("$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/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 45 
45  &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");  &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");  &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    
51  sub make_missing_probes  sub make_missing_probes

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