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Annotation of /FigKernelScripts/ma_pipeline.pl

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1 : overbeek 1.1 use strict;
2 :     use Data::Dumper;
3 :    
4 : overbeek 1.3 my $usage = "usage: ma_pipeline Genome RMA-key";
5 : overbeek 1.1
6 : overbeek 1.3 my($genome,$orgD);
7 : overbeek 1.1 (
8 : overbeek 1.3 ($genome = shift @ARGV) && ($orgD = "$FIG_Config::organisms/$genome")
9 : overbeek 1.1 )
10 :     || die $usage;
11 : overbeek 1.3
12 :     (-d $orgD) || die "invalid organism directory";
13 :    
14 :     (my $rma_key = shift @ARGV)
15 : overbeek 1.2 || die $usage;
16 : overbeek 1.1
17 :     my $exp_ed = "$orgD/UserSpace/ExpressionData";
18 :     (-d $exp_ed)
19 :     || die "Where is $exp_ed?";
20 :     (-s "$exp_ed/probes")
21 :     || die "Where is $exp_ed/probes?";
22 :     (-s "$orgD/contigs")
23 :     || die "Where is $orgD/contigs?";
24 :     (-s "$orgD/Features/peg/tbl")
25 :     || die "Where is $orgD/Features/peg/tbl?";
26 :    
27 : overbeek 1.3 &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 : overbeek 1.4 &run("remove_multiple_occurring_probes $exp_ed/peg.probe.table $exp_ed/probe.occ.table > $exp_ed/peg.probe.table.no.multiple");
29 : overbeek 1.3 system "pushd $exp_ed";
30 :     chdir $exp_ed;
31 :    
32 :     &run("Rscript $FIG_Config::bin/RunRMA.R $rma_key $exp_ed/peg.probe.table $exp_ed/Experiments 2> $exp_ed/stderr.RMA");
33 :     &run("$FIG_Config::bin/call_coregulated_clusters_on_chromosome $genome $exp_ed/raw_data.tab > $exp_ed/coregulated.clusters 2> $exp_ed/stderr.coregulated.clusters");
34 :     &run("$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");
35 : overbeek 1.7 &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");
36 : overbeek 1.5
37 : overbeek 1.7 &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");
38 :     &run("cut -f2 $exp_ed/probes.always.on > $exp_ed/pegs.always.on");
39 : overbeek 1.6 &run("Rscript $FIG_Config::bin/Pipeline.R $exp_ed/pegs.always.on $exp_ed/merged.clusters > $exp_ed/comments.by.Pipeline.R");
40 : overbeek 1.3 &run("Rscript $FIG_Config::bin/SplitGeneSets.R $exp_ed/merged.clusters 0.7 > $exp_ed/split.clusters");
41 :     system "popd";
42 :    
43 :     sub run {
44 :     shift if UNIVERSAL::isa($_[0],__PACKAGE__);
45 :     my($cmd) = @_;
46 : overbeek 1.2
47 : overbeek 1.3 if ($ENV{FIG_VERBOSE}) {
48 :     my @tmp = `date`;
49 :     chomp @tmp;
50 :     print STDERR "$tmp[0]: running $cmd\n";
51 :     }
52 :     (system($cmd) == 0) || die("FAILED: $cmd");
53 :     }
54 : overbeek 1.2

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