[Bio] / FigKernelScripts / compute_fasta_lengths.pl Repository:
ViewVC logotype

View of /FigKernelScripts/compute_fasta_lengths.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.1 - (download) (as text) (annotate)
Tue Sep 14 19:10:59 2010 UTC (9 years, 2 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, rast_rel_2010_0928, 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
Precompute fasta lengths for the non-FF nr.

#
# Given a fasta file, write a btree with the fasta lengths.
#

use DB_File;
use strict;
use gjoseqlib;

@ARGV == 2 or die "Usage: $0 fasta-file btree\n";

my $fasta = shift;
my $btree = shift;

open(FA, "<", $fasta) or die "Cannot open $fasta: $!";

my %len_btree;
unlink($btree);

my $len_btree_tie = tie %len_btree, 'DB_File', $btree, O_RDWR | O_CREAT, 0666, $DB_BTREE;

$len_btree_tie or die "Cannot create btree $btree: $!\n";

while (my($id, $def, $seq) = read_next_fasta_seq(\*FA))
{
    $len_btree{$id} = length($seq);
}
$len_btree_tie->sync();
untie %len_btree;

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3