[Bioperl-l] Next-gen modules

Peter Rice pmr at ebi.ac.uk
Wed Jun 24 07:48:23 EDT 2009

Peter wrote:
> On Tue, Jun 23, 2009 at 1:22 PM, Peter Rice<pmr at ebi.ac.uk> wrote:
>> The '-' names look nice though. We can consider introducing them. Do you
>> have a full list of format names (sequence, feature, alignment, etc.) we
>> can try to conform to?
> See http://biopython.org/wiki/SeqIO and http://biopython.org/wiki/AlignIO

Thanks. I'll take a look at those.

> Getting EMBOSS to conforming should be trivial - in general when
> picking a format name for Biopython's SeqIO or AlignIO (and we
> have avoided multiple aliases with one exception) we have tried to
> use anything shared by BioPerl and EMBOSS. The FASTQ variants
> are unusual in that Biopython got to invent some names.
> In future where would be a good place to discuss these kinds of
> cross-platform issues? (i.e. BioPerl, Biopython, EMBOSS, etc).

I was planning to suggest a get-together at BOSC in Stockholm so we can
identify common cross-platform issues. I'm sure there are many ways we
can conform with naming and interfaces and perhaps even share code.

>>>> We also allow the integer quality score format ... is anyone still
>>>> using that (it looks horrible to me :-)
>>> Do you mean the QUAL file format holding PHRED scores?
>>> Roche provide tools to turn their SFF files into FASTA and
>>> QUAL files, so they are still used.
>> Probably ... unless there is a Solexa version too.
> We may be talking at cross purposes here, this is QUAL format:
> http://www.bioperl.org/wiki/Qual_sequence_format

Yes that is different. We'll worry about separate QUAL files later (we
already find separate GFF files a pain for features) and still with the
"fastqint" format name.



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