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revision 1.10, Sun May 30 21:34:44 2010 UTC revision 1.11, Sat Jun 5 15:38:44 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  my $tbl = (-s "$exp_ed/tbl") ? "$exp_ed/tbl" : $orgD/Features/peg/tbl;  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");  &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;
# Line 40  Line 40 
40  &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");
41  &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");
42  &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 > $exp_ed/split.clusters");
43    &run("$FIG_Config::bin/compute_atomic_regulons $genome");
44    
45  sub make_missing_probes  sub make_missing_probes
46  {  {

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