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Annotation of /FigKernelScripts/ma_pipeline.pl

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Revision 1.2 - (view) (download) (as text)

1 : overbeek 1.1 use strict;
2 :     use Data::Dumper;
3 :    
4 : overbeek 1.2 my $usage = "usage: ma_pipeline OrgDir RMA-key";
5 : overbeek 1.1
6 :     my($orgD);
7 :     (
8 :     ($orgD = shift @ARGV)
9 :     )
10 :     || die $usage;
11 : overbeek 1.2 (my $rma_key = sift @ARGV)
12 :     || die $usage;
13 : overbeek 1.1
14 :     my $exp_ed = "$orgD/UserSpace/ExpressionData";
15 :     (-d $exp_ed)
16 :     || die "Where is $exp_ed?";
17 :     (-s "$exp_ed/probes")
18 :     || die "Where is $exp_ed/probes?";
19 :     (-s "$orgD/contigs")
20 :     || die "Where is $orgD/contigs?";
21 :     (-s "$orgD/Features/peg/tbl")
22 :     || 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";
25 : overbeek 1.2
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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