[Bio] / FortyEight / imp_prepare_sims.pl Repository:
ViewVC logotype

View of /FortyEight/imp_prepare_sims.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.1 - (download) (as text) (annotate)
Wed Sep 5 20:59:03 2007 UTC (12 years, 3 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, 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, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Rollup of RAST->SEED import stuff.

#
# Prepare for sims computation.
#
# Compute the differences in the new and old NR, and pull the fasta data.
#

use strict;
use FIG;
use FIG_Config;
use File::Basename;
use ImportJob;
use GenomeMeta;
use JobStage;

@ARGV == 1 or die "Usage: $0 job-dir\n";

my $jobdir = shift;

-d $jobdir or die "$0: job dir $jobdir does not exist\n";

my $stage = new JobStage('ImportJob', 'prepare_sims', $jobdir);

$stage or die "$0: Could not create job object";

$stage->log("Running on " . $stage->hostname);

$stage->set_status("running");
$stage->set_running("yes");

$stage->set_qualified_metadata("host", $stage->hostname);

#
# First compute the changes in ids.
#

my @cmd = ("$FIG_Config::bin/compute_changed_ids_for_nrs",
	   "$jobdir/prev_nr",
	   "$jobdir/prev_syn",
	   "$jobdir/nr",
	   "$jobdir/ids.added",
	   "$jobdir/ids.changed",
	   "$jobdir/ids.deleted");
$stage->run_process("compute_changed_ids_for_nrs", @cmd);

my $cmd = "$FIG_Config::bin/pull_fasta_entries $jobdir/nr < $jobdir/ids.added > $jobdir/seqs.added";

$stage->log("run $cmd");
my $rc = system($cmd);
if ($rc != 0)
{
    $stage->fatal("cmd failed with rc=$rc");
}

$stage->log("cmd completed");


$stage->log("completed");
$stage->set_running("no");
$stage->set_status("complete");


MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3