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Revision 1.2 - (download) (as text) (annotate)
Wed Sep 26 00:39:03 2007 UTC (12 years, 1 month 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
Changes since 1.1: +1 -1 lines
Import changes.

#
# Given a sims job directory, validate that each id in input file in the task list is present
# in the generated raw sims data in sims.raw/raw.XX. Note that the output fiel currently does
# not match the filename in the task.list, though it probably should.
#

use strict;
use FIG;
use FileHandle;
use FIG_Config;
use File::Copy;
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 $simdir = "$jobdir/sims.job";

open(TASK, "<$simdir/task.list") or die("Cannot open task list $simdir/task.list: $!");

my $errors;

while (<TASK>)
{
    chomp;
    my($id, $in, $nr, $args, $out, $err) = split(/\t/);

    if ($in !~ m,^/,)
    {
	$in = "$jobdir/$in";
    }
    if (!open(IN, "<$in"))
    {
	warn "Cannot open input file $in: $!";
	$errors++;
	next;
    }

    my %ids;
    {
	local $/ = "\n>";
	
	while (<IN>)
	{
	    if (/^>?(\S+)/)
	    {
		$ids{$1}++;
	    }
	}
	close(IN);
    }

    my $sims = $out;
    if (!open(SIMS, "<$sims"))
    {
	warn "Cannot open sims file $sims: $!";
	$errors++;
	next;
    }
    print "$sims\n";
    while (<SIMS>)
    {
	if (/^(\S+)/ and $ids{$1})
	{
	    delete $ids{$1};
	}
    }
    close(SIMS);
    if (%ids)
    {
	warn "Task $id missing sims\t", join("\t", keys %ids), "\n";
	$errors++;
    }
}

if ($errors)
{
    die "$errors errors occurred during validation\n";
}

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