[Biopython] pd.df.to_csv(..., compression="bgzip")?

[Peter Cock]

Yes. BGZF is just a special kind of GZIP file, if all you are doing is
decompressing it for reading it then the standard gzip.open(...)
is fine.

Peter


On Wed, Mar 13, 2024 at 10:03 AM Dan Bolser <dan.bolser at outsee.co.uk> wrote:

> bgzip is a 'bio' thing, so thought I'd ask here. It's perhaps not
> 'biopython', but it's bio/python.
>
> On Tue, 12 Mar 2024 at 19:11, Sean Brimer <skbrimer at gmail.com> wrote:
>
>> Hi Dan,
>>
>> This feels more like a panda's issue than a biopython issue. That said, I
>> think you could just use gzip. I think. bgzip for samtools was built on top
>> of gzip so it probably decompresses in a similar way.
>>
>> On Tue, Mar 12, 2024 at 12:52 PM Dan Bolser <dan.bolser at outsee.co.uk>
>> wrote:
>>
>>> Hi,
>>>
>>> I can pass `compression="gzip"` to pandas.DataFrame.to_csv, but not
>>> bgzip... how to update pandas to support bgzip?
>>>
>>>
>>> Thanks,
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