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revision 1.1, Mon Apr 19 20:22:16 2010 UTC revision 1.2, Wed May 5 15:17:38 2010 UTC
# Line 1  Line 1 
1  use strict;  use strict;
2  use Data::Dumper;  use Data::Dumper;
3    
4  my $usage = "usage: ma_pipeline OrgDir";  my $usage = "usage: ma_pipeline OrgDir RMA-key";
5    
6  my($orgD);  my($orgD);
7  (  (
8   ($orgD = shift @ARGV)   ($orgD = shift @ARGV)
9   )   )
10      || die $usage;      || die $usage;
11    (my $rma_key = sift @ARGV)
12        || die $usage;
13    
14  my $exp_ed = "$orgD/UserSpace/ExpressionData";  my $exp_ed = "$orgD/UserSpace/ExpressionData";
15  (-d $exp_ed)  (-d $exp_ed)
# Line 20  Line 22 
22      || die "Where is $orgD/Features/peg/tbl?";      || die "Where is $orgD/Features/peg/tbl?";
23    
24  system "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";  system "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";
25    
26    system "Rscript $FIG_Config::bin/RunRMA.R $rma_key $exp_ed/peg.probe.table $exp_ed/Experiments 2> $exp_ed/stderr.RMA";
27    
28    system "$FIG_Config::bin/call_coregulated_clusters_on_chromosome $genome $exp_ed/raw_data.tab > $exp_ed/coregulated.clusters 2> $exp_ed/stderr.coregulated.clusters";
29    system "$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";
30    system "cat $exp_ed/coregulated.clusters $exp_ed/coregulated.subsys | cut -f1 | $FIG_Config::bin/merge_gene_sets > $exp_ed/merged.clusters";
31    system "Rscript $FIG_Config::bin/Pipeline.R $exp_ed/merged.clusters 0.7 > $exp_ed/comments.by.Pipeline.R";
32    system "Rscript $FIG_Config::bin/SplitGeneSets.R $exp_ed/merged.clusters 0.7 > $exp_ed/split.clusters";

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