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Revision 1.3 - (download) (as text) (annotate)
Sun Feb 24 15:21:29 2013 UTC (6 years, 8 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2014_0912, rast_rel_2014_0729, HEAD
Changes since 1.2: +2 -2 lines
compute correspondences for a pan genome

use strict;
use Data::Dumper;

my $usage = "usage: ma_pipeline_ecoli";

my $orgD = '/home/overbeek/Proj/FIGdisk/FIG/Data/Organisms/83333.1';
my $exp_ed = "$orgD/UserSpace/ExpressionData";
(-d $exp_ed)
    || die "Where is $exp_ed?";
(-s "$exp_ed/probes")
    || die "Where is $exp_ed/probes?";
(-s "$orgD/contigs")
    || die "Where is $orgD/contigs?";
(-s "$orgD/Features/peg/tbl")
    || die "Where is $orgD/Features/peg/tbl?";
($orgD =~ /(\d+\.\d+)$/)
    || die "Organism directory must end in organism ID";
my $genome = $1;

# system "$FIG_Config::bin/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";
chdir $exp_ed;
system "Rscript $FIG_Config::bin/RunRMA.R Ecoli_ASv2 $exp_ed/peg.probe.table $exp_ed/Experiments 2> $exp_ed/stderr.RMA";
#

system "$FIG_Config::bin/call_coregulated_clusters_on_chromosome $genome $exp_ed/raw_data.tab > $exp_ed/coregulated.clusters 2> $exp_ed/stderr.coregulated.clusters";
system "$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";
system "cat $exp_ed/coregulated.clusters $exp_ed/coregulated.subsys | cut -f1 | $FIG_Config::bin/merge_gene_sets > $exp_ed/merged.clusters";
system "Rscript $FIG_Config::bin/Pipeline.R $exp_ed/merged.clusters 0.7 > $exp_ed/comments.by.Pipeline.R";
system "Rscript $FIG_Config::bin/SplitGeneSets.R $exp_ed/merged.clusters 0.7 > $exp_ed/split.clusters";

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