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Revision 1.2 - (download) (as text) (annotate)
Mon Apr 16 21:42:31 2007 UTC (12 years, 7 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, 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, 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: +15 -2 lines
compute length btree also

use strict;
use DB_File;

#
# Create a btree indexed version of the given NR.
#

my $usage = "index_nr nr-file  index-nr-file length-nr-index";

@ARGV == 3 or die $usage;

my $nr = shift;
my $inr = shift;
my $lnr = shift;

open(NR, "<$nr") or die "Cannot open NR $nr: $!\n";

my %idx;

my $db = tie %idx, "DB_File", $inr, O_RDWR | O_CREAT, 0666, $DB_BTREE;
$db or die "Cannot create btree $inr: $!\n";

my %lidx;

my $ldb = tie %lidx, "DB_File", $lnr, O_RDWR | O_CREAT, 0666, $DB_BTREE;
$ldb or die "Cannot create btree $lnr: $!\n";


$/ = "\n>";
while (defined($_ = <NR>))
{
    chomp;
    if ($_ =~ /^>?(\S+)[^\n]*\n(.*)/s)
    {
	my $id  =  $1;
	my $seq =  $2;
	$seq =~ s/\s//gs;
	$idx{$id} = $seq;
	$lidx{$id} = length($seq);
    }
    if ($. % 100000 == 0)
    {
	print "$.\n";
    }
}
close(NR);
$db->sync();
untie %idx;
$ldb->sync();
untie %lidx;



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