[Open-bio-l] Mixed case sequence strings in FASTQ?

[Peter]

On Wed, Aug 12, 2009 at 12:32 AM, Chris Fields<cjfields at illinois.edu> wrote:
>
> On Aug 10, 2009, at 8:06 AM, Peter wrote:
>
>> On Mon, Aug 10, 2009 at 2:02 PM, Peter Rice<pmr at ebi.ac.uk> wrote:
>>>
>>> Peter C. wrote:
>>>
>>>> I would suggest that OBF tools all treat the sequence in FASTQ files
>>>> as is, and preserve the case on output.
>>>>
>>>> Any thoughts?
>>>
>>> EMBOSS does that with all sequence formats. The case of the original
>>> sequence is preserved and reproduced on output. We have not specified
>>> upper or lower case only for any of our current output formats.
>>>
>>> We provide command line options to force sequences to be converted to
>>> upper or lower case if the user want to specify one or the other -
>>> usually just to convert sequences for post processing by some other tool.
>>
>> Cool. It looks like we are on the same wavelength here :)
>>
>> Peter
>
> I believe so (sorry about lack of responsiveness, just got back in town).
>
> chris

Great - I've added some unit test code in Biopython to confirm we
leave the sequence case as-is on a loading and saving FASTQ files.

Peter