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Revision 1.5 - (download) (as text) (annotate)
Thu Jun 19 16:23:34 2014 UTC (5 years, 4 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2014_0729, rast_rel_2014_0912, HEAD
Changes since 1.4: +18 -0 lines
added some documentation

# This pipeline requires that you build a Data directory used to retain all
# relevant files.  Initially,
#
#  1. Data/genome is a file containing a single line, which has the
#     genome ID (e.g., 83333.1)
#
#  2. Data/aliases is a file containing 3-tuples: [PEG,Gene,Locus]
#     If you do not have gene/locus data, make all three fields the
#     PEG Id.
#
#  3. Data/roles.always.on is a file containing 1 role per line.
#     These are a list of the roles that are expected to be ON in
#     the vast majority of samples.
#
#  4. Data/gene.locus.exp.val.tuples must contain the expression values
#     for the different samples: [Gene,Locus,Sample,ExpressionValue]


use Data::Dumper;
use File::Basename;
use Getopt::Long;
use SeedEnv;
use strict;

my $usage = "usage: ex_pipeline -d DataDir\n";
my($i,$j);
my $dataD;
my $rc  = GetOptions('d=s' => \$dataD);

if ((! $rc) || (! -d $dataD))
{ 
    print STDERR $usage; exit ;
}
(-s "$dataD/genome") || die "you need to put a 'genome' file into $dataD";
(-s "$dataD/aliases") || die "you need to put a 'aliases' file into $dataD";
(-s "$dataD/roles.always.on") || die "you need to put a 'roles.always.on' file into $dataD";

if (! -s "$dataD/aliases.with.function")
{
    &SeedUtils::run("svr_function_of -c 1 < $dataD/aliases > $dataD/aliases.with.function");
}
if (! -s "$dataD/locus.pccs")
{
    &SeedUtils::run("ex_compute_pccs -d $dataD");
}

if (! -s "$dataD/coreg.based.on.clusters")
{
    &SeedUtils::run("ex_get_adjacency_based_estimates -d $dataD");
}
if (! -s "$dataD/coreg.based.on.subsystems")
{
    &SeedUtils::run("ex_get_subsystem_based_estimates -d $dataD > $dataD/coreg.based.on.subsystems");
}
if (! -s "$dataD/peg.on.off.calls")
{
    &SeedUtils::run("ex_make_on_off_calls -d $dataD");
}
if (! -s "$dataD/initial.atomic.regulons")
{
    &SeedUtils::run("ex_make_initial_atomic_regulons -d $dataD");
}
if (! -s "$dataD/atomic.regulons")
{
    &SeedUtils::run("ex_split_atomic_regulons -d $dataD");
}
&SeedUtils::run("ex_set_on_off_for_atomic_regulons -d $dataD");
&SeedUtils::run("ex_adjust_peg_on_off -d $dataD");
&SeedUtils::run("ex_fillout_ar_data -d $dataD");
&SeedUtils::run("ex_rare_ar_and_pegs -d $dataD");
&SeedUtils::run("ex_add_conditions -d $dataD");

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