[Bioperl-l] indexed fastq files
avilella at gmail.com
Wed Feb 24 06:45:23 EST 2010
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,
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"?
> 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.
>> 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?
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
More information about the Bioperl-l