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Revision 1.1 - (download) (as text) (annotate)
Thu May 1 22:33:17 2008 UTC (12 years 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, myrast_rel40, 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, 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
Index scripts for FIGV accleration.

#
# 
# Create btree index of assigned_functions and annotations for use with FIGV.
#
# This does not currently use the multiple assigned_function files as RAST generates;
# it is currently intended for large metagenome directories.
#

use FIG;
use FIG_Config;
use strict;
use DB_File;
use Data::Dumper;

@ARGV == 1 or die "Usage: $0 orgdir\n";

my $dir = shift;

-d $dir or die "Given directory $dir is not a directory\n";

my $assigns = "$dir/assigned_functions";
my $annos = "$dir/annotations";

open(ASSIGN, "<", $assigns) or die "Cannot open $assigns: $!";
open(ANNO, "<", $annos) or die "Cannot open $annos: $!";

my $assign_btree = "$assigns.btree";
my $anno_btree = "$annos.btree";

my(%anno, %assign, $anno_tie, $assign_tie);

if (-f $anno_btree)
{
    unlink($anno_btree);
}

if (-f $assign_btree)
{
    unlink($assign_btree);
}

my $anno_tie = tie %anno, 'DB_File', $anno_btree, O_RDWR | O_CREAT, 0666, $DB_BTREE;
$anno_tie or die "Cannot tie $anno_btree: $!";

my $assign_tie = tie %assign, 'DB_File', $assign_btree, O_RDWR | O_CREAT, 0666, $DB_BTREE;
$assign_tie or die "Cannot tie $assign_btree: $!";

while (<ASSIGN>)
{
    chomp;
    my($fid, $assign) = split(/\t/);
    $assign{$fid} = $assign;
}
close(ASSIGN);

$/ = "//\n";

while (<ANNO>)
{
    chomp;
    if (/^(fig\S+)/)
    {
	$anno{$1} = $_;
    }
}

untie $anno_tie;
untie $assign_tie;

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