[Bio] / FigKernelScripts / ma_pipeline.pl Repository:
ViewVC logotype

View of /FigKernelScripts/ma_pipeline.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.2 - (download) (as text) (annotate)
Wed May 5 15:17:38 2010 UTC (9 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.1: +11 -1 lines
fixes to pipeline

use strict;
use Data::Dumper;

my $usage = "usage: ma_pipeline OrgDir RMA-key";

my($orgD);
(
 ($orgD = shift @ARGV)
 )
    || die $usage;
(my $rma_key = sift @ARGV) 
    || die $usage;

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?";

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";

system "Rscript $FIG_Config::bin/RunRMA.R $rma_key $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";

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3