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Revision 1.1 - (download) (as text) (annotate)
Tue Jul 17 20:28:06 2007 UTC (12 years, 4 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
Utility for creating btree access for fasta files.

#
# Create a btree containing the sequences in a fasta file.
#
#

my $usage = "make_fasta_btree fasta-file btree-file len-btree-file";

use strict;
use FIG;
use DB_File;

@ARGV == 3 or die $usage;

my $fasta_file = shift;
my $btree_file = shift;
my $len_btree_file = shift;

open(FA, "<$fasta_file") or die "Cannot open $fasta_file: $!";
#
# Unlink existing file to ensure it is clean.
#
if (-f $btree_file)
{
    unlink($btree_file);
}
if (-f $len_btree_file)
{
    unlink($len_btree_file);
}

my %btree;
my $btree_tie = tie %btree, 'DB_File', $btree_file, O_RDWR | O_CREAT, 0666, $DB_BTREE;

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

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

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

my($seqp, $id, $comment);

while (($id, $seqp, $comment) = &FIG::read_fasta_record(\*FA))
{
    $btree{$id} = $$seqp;
    $len_btree{$id} = length($$seqp);
}
untie %btree;

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