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

[Dan Bolser]

pandas.to_csv is the function that writes data. pandas.read_csv silently
handles decompression as needed.



On Wed, Mar 13, 2024, 10:49 AM Peter Cock <p.j.a.cock at googlemail.com> wrote:

> 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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>>>>
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>
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