[Bioperl-guts-l] [Bug 2577] New: Bio::Assembly and Bio::Assembly::IO can exceed the set open file ulimit

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2577

           Summary: Bio::Assembly and Bio::Assembly::IO can exceed the set
                    open file ulimit
           Product: BioPerl
           Version: main-trunk
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: cjfields at bioperl.org


Bio::Assembly::IO is capable of exceeding the 'ulimit -n' (open files) for the
system.  This primarily occurs through the creation of too many
Bio::SeqFeature::Collection instances within a Bio::Assembly::Contig, each
which has a tied DB_File filehandle.  For a more involved explanation see bug
2320.

The following script illustrates the problem (adjust the for loop end range
value to exceed the 'ulimit -n' limit for open files).

#!/usr/bin/perl -w

use strict;
use warnings;
use Bio::Assembly::Contig;

my @contigs;
push @contigs, Bio::Assembly::Contig->new()
    for (1..10000);


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