[Bioperl-l] Next-gen modules

[Chris Fields]

On Jul 24, 2009, at 8:00 AM, Peter wrote:

> Hi all,
>
> On Fri, Jul 24, 2009 at 1:19 PM, Chris Fields<cjfields at illinois.edu>  
> wrote:
>>>
>>> Have you guys (BioPerl) have also gone for "fastq-sanger" instead of
>>> just "fastq" for the Sanger Standard version of FASTQ (like EMBOSS)?
>>> Does BioPerl use just "fastq" to mean anything?
>>
>> Short answer: yes, and yes.
>>
>> Slightly longer answer: I've set up SeqIO so it converts "new(- 
>> format =>
>> 'foo-bar')" to new(-format => 'foo, -variant => 'bar').  In the fastq
>> constructor, if the variant is expected but isn't defined (i.e. for  
>> 'fastq')
>> it defaults to sanger.  Makes it a bit easier maintenance-wise if a  
>> new
>> variant pops up.
>
> Right, so BioPerl understands "fastq" and "fastq-sanger" to mean the
> Sanger standard FASTQ files.

Yes.

> I've just updated Biopython to also allow "fastq-sanger" as an alias  
> for
> "fastq", so we are consistent here:
> http://lists.open-bio.org/pipermail/biopython-dev/2009-July/ 
> 006466.html
>
> Biopython, BioPerl and EMBOSS now all agree on the format names:
> * "fastq-sanger" - PHRED scores offset 33
> * "fastq-solexa" - Solexa scores offset 64
> * "fastq-illumina" - PHRED scores offset 64
>
> And Biopython and BioPerl also agree on the meaning of "fastq" as
> an alias for "fastq-sanger". Unfortunately EMBOSS differs here, see:
> http://lists.open-bio.org/pipermail/emboss-dev/2009-July/000599.html
>
> Does BioJava or BioRuby have a SeqIO equivalent where they need
> to give different sequence formats unique names? If so, we should
> talk to them soon...
>
> Peter

Not sure, but it would be nice to have consistency there, yes.

chris