[Bioperl-guts-l] [Bug 1376] New: Storable freeze doesn't properly serialize Seq objects

bugzilla-daemon at cvs.open-bio.org bugzilla-daemon at cvs.open-bio.org
Sun Feb 2 15:11:03 EST 2003


           Summary: Storable freeze doesn't properly serialize Seq objects
           Product: Bioperl
           Version: main-trunk
          Platform: Macintosh
        OS/Version: MacOS X
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: jason at open-bio.org
                CC: lstein at cshl.org

Using Storable's freeze in Bio::DB::FileCache will not allow a Bio::Seq's associated Bio::Species object to be properly frozen or thawed.  This only seems to happen if the program exits and reuses the cache file.

Basic code to replicate (run this snippet twice).

my $db = new Bio::DB::FileCache(-seqdb => Bio::DB::GenPept->new(), -keep => 1, -file=>'/tmp/gp.idx');

my $seq = $db->get_Seq_by_id('17531227');

print $seq->species->common_name, "\n";

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