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

View of /FigKernelScripts/ma_pipeline_ecoli.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.2 - (download) (as text) (annotate)
Tue Apr 27 16:40:46 2010 UTC (9 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, myrast_rel40, mgrast_dev_05262011, mgrast_dev_04082011, rast_rel_2010_0928, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2010_0526, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2011_0119, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, mgrast_dev_04012011, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_02222011, mgrast_dev_10262011
Changes since 1.1: +7 -7 lines
pipeline for Ecoli

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/EcoliRMA.R $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