[Bioperl-l] indexed fastq files

[Albert Vilella]

BTW, I should mention that my index file was created with this options
on the same linux system:

my $db  = Bio::Index::Fastq->new(-filename => $fastafile,
-dbm_package=>'DB_File');

So it looks more like DB_File dependent than "Win DB_File"...

On Wed, Feb 24, 2010 at 11:32 AM, Albert Vilella <avilella at gmail.com> wrote:
> Hi Chris,
>
> I am finding that Bio::Index::Fastq seek is chopping off the first
> character of the fastq entry. I'm on Linux using bioperl-1.6.1 and
> debugged the problem to this point in AbstractSeq.pm:143, where there
> is this funny commented line:
>
>                # $begin-- if( $^O =~ /mswin/i); # workaround for Win DB_File bug
>                seek($fh, $begin, 0);
>
> If I apply this $begin--, everything works fine, but I am not using
> windows, I am on a Linux cluster.
>
> Any ideas why this was tagged as a "Win DB_File bug"?
>
> Cheers,
>
> Albert.
>
> On Mon, Jan 4, 2010 at 9:59 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> Bio::Index::Fastq, maybe?  To tell the truth, I haven't tried it since we refactored FASTQ parsing, so let us know if it doesn't work.
>>
>> chris
>>
>> On Jan 4, 2010, at 2:00 PM, Albert Vilella wrote:
>>
>>> Hi all,
>>>
>>> What is the best way to index fastq files, so that once clustered, I
>>> can provide a list of seq_ids and get
>>> them back in fastq format from the indexed db?
>>>
>>> Cheers,
>>>
>>> Albert.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>