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Revision 1.3 - (view) (download) (as text)
| 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 : | |||
| 29 : | 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 : | &run("cat $exp_ed/coregulated.clusters $exp_ed/coregulated.subsys | cut -f1 | $FIG_Config::bin/merge_gene_sets > $exp_ed/merged.clusters"); | ||
| 36 : | &run("Rscript $FIG_Config::bin/Pipeline.R $exp_ed/merged.clusters 0.7 > $exp_ed/comments.by.Pipeline.R"); | ||
| 37 : | &run("Rscript $FIG_Config::bin/SplitGeneSets.R $exp_ed/merged.clusters 0.7 > $exp_ed/split.clusters"); | ||
| 38 : | system "popd"; | ||
| 39 : | |||
| 40 : | sub run { | ||
| 41 : | shift if UNIVERSAL::isa($_[0],__PACKAGE__); | ||
| 42 : | my($cmd) = @_; | ||
| 43 : | overbeek | 1.2 | |
| 44 : | overbeek | 1.3 | if ($ENV{FIG_VERBOSE}) { |
| 45 : | my @tmp = `date`; | ||
| 46 : | chomp @tmp; | ||
| 47 : | print STDERR "$tmp[0]: running $cmd\n"; | ||
| 48 : | } | ||
| 49 : | (system($cmd) == 0) || die("FAILED: $cmd"); | ||
| 50 : | } | ||
| 51 : | overbeek | 1.2 |
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