[Bioperl-guts-l] [Bug 2823] New: Bio::SeqIO::embl->next_seq corrupted with "Segmentation fault" when parsing million-line entries

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon May 4 07:38:55 EDT 2009


http://bugzilla.open-bio.org/show_bug.cgi?id=2823

           Summary: Bio::SeqIO::embl->next_seq corrupted with "Segmentation
                    fault" when parsing million-line entries
           Product: BioPerl
           Version: 1.6 branch
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: blocker
          Priority: P2
         Component: Bio::SeqIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: brianli.cas at gmail.com


Platform: 
BioPerl 1.6.0
Perl 5.8.8
Ubuntu 8.04 LTS Server 64-bit version (Linux 2.6.24-23-server)

When parsing EMBL file rel_ann_mus_01_r99.dat which has big million-line
entries, Bio::SeqIO::embl->next_seq gives "Segmentation fault". This happens
when tring to get the first entry with next_seq.

An zipped version of the data file I tried to parse is available at
ftp://bio-mirror.net/biomirror/embl/release/rel_ann_mus_01_r99.dat.gz

# The code I use
my $seqio = Bio::SeqIO->new(-file => 'rel_ann_mus_01_r99.dat',
                            -format => 'EMBL');
my $index = 1;
while (my $seq = $seqio->next_seq)
{
    print "Dealing with entry: $index\n";
    # Some parse process
    $index++;
}
# end of code


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