[Bioperl-l] Next-gen modules
cjfields at illinois.edu
Fri Jul 24 14:27:32 EDT 2009
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>
>>> 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
>> it defaults to sanger. Makes it a bit easier maintenance-wise if a
>> variant pops up.
> Right, so BioPerl understands "fastq" and "fastq-sanger" to mean the
> Sanger standard FASTQ files.
> I've just updated Biopython to also allow "fastq-sanger" as an alias
> "fastq", so we are consistent here:
> 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:
> 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...
Not sure, but it would be nice to have consistency there, yes.
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