[Bioperl-l] Fastq - is it flush, or not?

[Chris Fields]

The error appears to be in revcom(), so my guess is something with clipping of the quality data?  Hard so say for sure, though, w/o seeing the data and testing it.  

chris

On Jul 11, 2011, at 3:47 AM, Nestor Zaburannyi wrote:

> Dear All.
> 
> I need to reverse-complement a huge *.fastq file. I try to
> 
> while (my $seq = $in->next_seq)
>    {
>    $out->write_seq($seq->revcom);
>    }
> 
> However, it stops with:
> 
> ------------- EXCEPTION -------------
> MSG: Can not get a reverse complement. The object is not flush.
> STACK Bio::Seq::Meta::Array::revcom /usr/share/perl5/Bio/Seq/Meta/Array.pm:648
> 
> 
> Adding
> 
> $seq->force_flush('1');
> 
> helps, but is it necessary and proper way? Sequences seem to be "flush".
> 
> Sincerely yours
> Nestor
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l