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Revision 1.1 - (download) (as text) (annotate)
Tue Nov 9 22:14:29 2010 UTC (9 years, 4 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, mgrast_dev_05262011, mgrast_dev_04082011, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2014_0729, 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, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_02222011, mgrast_dev_10262011, HEAD
New FIGfam merge code.

# Process a list of genome ids to generate an updated FIGfams families.2c file.

use strict;
use SeedUtils;
use FIG_Config;

@ARGV == 3 or @ARGV == 4
    or die "Usage: FFB2_genome_group_pipeline genome-list-file old.families.2c new.families.2c [workdir]\n";

my $genome_list = shift;
my $oldFF = shift;
my $newFF = shift;
my $workdir = shift;

my $tmpdir;
if (-d $workdir)
    $tmpdir = $workdir;
    $tmpdir = "$FIG_Config::temp/tmp.$$";

SeedUtils::run("$FIG_Config::bin/FFB2_create_binary_relationships $genome_list > $tmpdir/binary_relationships 2> $tmpdir/create_binary_relationships.err");

SeedUtils::run("$FIG_Config::bin/cluster_objects < $tmpdir/binary_relationships > $tmpdir/clusters 2> $tmpdir/cluster_objects.err");

SeedUtils::run("$FIG_Config::bin/FFB2_merge_families_based_on_genus_groups $oldFF $tmpdir/clusters $newFF > $tmpdir/merge.out 2> $tmpdir/merge.err");

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