[Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO

Abhishek Pratap abhishek.vit at gmail.com
Sat Jul 10 16:38:06 EDT 2010


Thanks guys. Time to update my Bioperl. I will do that and report if I face
issues.

-A

On Sat, Jul 10, 2010 at 3:23 PM, Chris Fields <cjfields at illinois.edu> wrote:

> On Jul 10, 2010, at 6:44 AM, Peter wrote:
>
> > On Sat, Jul 10, 2010 at 12:43 PM, Peter <biopython at maubp.freeserve.co.uk>
> wrote:
> >> On Fri, Jul 9, 2010 at 4:02 PM, Abhishek Pratap <abhishek.vit at gmail.com>
> wrote:
> >>> Hi (Chris)
> >>>
> >>> I feel I might be hitting a bug or missing something. I am trying to
> convert
> >>> a raw FASTQ from ASCII-64 to ASCII-33.  I am copying the actual code
> and IO
> >>> for more clarity. I think the quality line is missing and the read is
> >>> breaking into two lines.
> >>>
> >>> Any obvious mistakes ?
> >>>
> >>> Thanks!
> >>> -Abhi
> >>
> >> It looks like you are getting FASTQ out rather than FASTQ (notice in
> addition to
> >> missing the qualities, the record starts with ">" rather than "@".
> >
> > Typo: FASTA out rather than FASTQ. The A and Q keys are too close
> together ;)
> >
> > Peter
>
> You have to be using a version of BioPerl that supports this.  The previous
> version of the FASTQ parser released prior to refactoring returned FASTA
> when using write_seq(), which was a significant bug that was fixed during
> the complete overhaul prior to the FASTQ paper.  My guess is the version of
> BioPerl is old and this is the module version being used.
>
> chris
>
> PS - Peter, had several very good mentions of this work from all
> Bio*/EMBOSS talks at BOSC, so a great success!


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