[Bioperl-l] BerkeleyDB

shalu sharma sharmashalu.bio at gmail.com
Fri Jan 25 15:18:18 UTC 2019


Hey everyone,
     So I am using this BerkeleyDB to make a huge database (tree method).
I use it to pull out matching ids (its working fine) from multiple datasets.
 here are few lines of the code:

use strict ;

use BerkeleyDB ;

use Bio::SeqIO;

my $filename = "tree" ;

unlink $filename ;

my %h ;

tie %h, 'BerkeleyDB::Btree',

                -Filename   => $filename,

                -Flags      => DB_CREATE,

    or die "Cannot open $filename: $!\n" ;


 # Add a key/value pair to the file

open(IN,"$ARGV[0]");                    # adding values

while(<IN>){

     my $line = $_;

     chomp($line);

     my @f = split('\t',$line);

     my $id = $f[0];my $val = $f[1];$id =~ s/^\s+//;$id =~ s/\s+$//;

     $val =~ s/^\s+//;$val =~ s/\s+$//;

     $h{$id} = $val;
----
----
My question is that: It makes a huge tree file. Is it possible to re-use
that tree file again instead of making it again and again. My query
datasets changes but not that database.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/bioperl-l/attachments/20190125/c8c6945a/attachment.html>


More information about the Bioperl-l mailing list