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

Chris Fields cjfields at illinois.edu
Sat Jul 10 15:23:30 EDT 2010


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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