[Open-bio-l] More FASTQ examples for cross project testing

[Chris Fields]

On Sep 1, 2009, at 10:28 AM, Peter wrote:

> On Wed, Aug 26, 2009 at 11:04 PM, Peter<biopython at maubp.freeserve.co.uk 
> > wrote:
>>
>> I didn't want to clog up the mailing list with attachments, but just
>> for the record, I've sent my first attempt at this to Peter (EMBOSS)
>> and Chris (BioPerl) for comment (and checking).
>
> I've emailed the latest test cases (off the mailing list) to Peter
> (EMBOSS), Chris (BioPerl), Michael (BioJava) and Naohisa
> (BioRuby). These files are also in Biopython's repository.
>
> I've just run these against bioperl-live SVN, and most of them
> work as I would expect. Note that the output of Solexa FASTQ
> files where the scores must be converted from PHRED values
> isn't working yet (Chris knows about this):
> http://lists.open-bio.org/pipermail/bioperl-l/2009-August/031064.html
>
> All the error_*.fastq files are correctly rejected by BioPerl, except
> those with invalid characters in the quality string (e.g. a delete)
> which are treated as a warning condition (rather than aborting
> with an exception):
>
> error_qual_del.fastq
> error_qual_escape.fastq
> error_qual_null.fastq
> error_qual_space.fastq
> error_qual_tab.fastq
> error_qual_unit_sep.fastq
> error_qual_vtab.fastq
>
> Presumably this is in line with (Bio)Perl norms? i.e. Make a best  
> guess
> at what the file is trying trying to say, issue a warning, but  
> continue?
>
> In Biopython (in line with Python norms), we don't try to guess.  
> Giving
> an error and aborting is the only clear and unambiguous action.
>
> Would it suffice to agree that all the OBF projects will read these
> error_*.fastq files and either raise an exception (abort), or at least
> issue a warning?
>
> Peter

I would rather throw on those; I can easily change that behavior to do  
whatever the consensus is.

chris