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Revision 1.1 - (download) (as text) (annotate)
Wed Oct 31 23:20:32 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
Determine NMPDR group name for given genome name.

use strict;
use FIG_Config;
use Data::Dumper;

my $usage = "get_nmpdr_group genus species";

if (@ARGV == 1)
{
    @ARGV = split(/\s+/, $ARGV[0]);
}

@ARGV >= 2 or die $usage;
my $genus = shift;
my $species = shift;

my $genus_species = "$genus $species";

my $nmpdr_data = parse_nmpdr_groups("$FIG_Config::fortyeight_data/NMPDR.GROUPS");

my $sm = $nmpdr_data->{species_match}->{$genus_species};

if ($sm ne "")
{
    print "$sm\n";
    exit 0;
}

my $gm = $nmpdr_data->{genus_match}->{$genus};
if ($gm ne "")
{
    print "$gm\n";
    exit 0;
}
exit 1;

#
# Parse the NMPDR group definitions.
#

sub parse_nmpdr_groups
{
    my($group_file) = @_;

    open(GF, "<$group_file") or die "cannot open nmpdr group file $group_file: $!";

    my $dat = {};
    while (<GF>)
    {
	chomp;
	my $groupname;
	s/^\s+//;
	s/\s+$//;
	if (/^(.*)\s+=>\s+(.*)/)
	{
	    $groupname = $2;
	    $_ = $1;
	}
	if (/^([a-z]+)\s+(\S+)/)
	{
	    $groupname = $_ unless $groupname;
	    $dat->{genus_match}->{$2} = $groupname;
	}
	else
	{
	    $groupname = $_ unless $groupname;
	    $dat->{species_match}->{$_} = $groupname;
	}
    }
#    print Dumper($dat);

    return $dat;
    
}


#
# Process any NMPDR marking for this job.
#

sub process_nmpdr
{
}


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