Re: [Biopython] pd.df.to_csv(..., compression="bgzip")?
Dan Bolser <[email protected]> Wed, 13 Mar 2024 10:04:34 +0000
| Newsgroups | gmane.comp.python.bio.general |
|---|---|
| Message-ID | <CANs1yP+A1wh_QYbDL7FsrjJOeWkek1xnRYwdTQeSkR6NJWUJYw@mail.gmail.com> |
--===============0757646579205830303== Content-Type: multipart/alternative; boundary="000000000000a93bd5061387e35b" --000000000000a93bd5061387e35b Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable 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 <[email protected]> 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 t= op > of gzip so it probably decompresses in a similar way. > > On Tue, Mar 12, 2024 at 12:52=E2=80=AFPM Dan Bolser <[email protected]= .uk> > wrote: > >> Hi, >> >> I can pass `compression=3D"gzip"` to pandas.DataFrame.to_csv, but not >> bgzip... how to update pandas to support bgzip? >> >> >> Thanks, >> _______________________________________________ >> Biopython mailing list - [email protected] >> https://mailman.open-bio.org/mailman/listinfo/biopython >> > --000000000000a93bd5061387e35b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr">bgzip is a 'bio' thing, so thought I'd ask her= e. It's perhaps not 'biopython', but it's bio/python.</div>= <br><div class=3D"gmail_quote"><div dir=3D"ltr" class=3D"gmail_attr">On Tue= , 12 Mar 2024 at 19:11, Sean Brimer <<a href=3D"mailto:[email protected]= m">[email protected]</a>> wrote:<br></div><blockquote class=3D"gmail_qu= ote" style=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,20= 4);padding-left:1ex"><div dir=3D"ltr"><div>Hi Dan, <br></div><div><br></div= ><div>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 bui= lt on top of gzip so it probably decompresses in a similar way. <br></div><= /div><br><div class=3D"gmail_quote"><div dir=3D"ltr" class=3D"gmail_attr">O= n Tue, Mar 12, 2024 at 12:52=E2=80=AFPM Dan Bolser <<a href=3D"mailto:da= [email protected]" target=3D"_blank">[email protected]</a>> wr= ote:<br></div><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px= 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir=3D= "ltr">Hi,<div><br></div><div>I can pass `compression=3D"gzip"` to= pandas.DataFrame.to_csv, but not bgzip... how to update pandas to support = bgzip?</div><div><br></div><div><br></div><div>Thanks,</div></div> _______________________________________________<br> Biopython mailing list=C2=A0 -=C2=A0 <a href=3D"mailto:Biopython@biopython.= org" target=3D"_blank">[email protected]</a><br> <a href=3D"https://mailman.open-bio.org/mailman/listinfo/biopython" rel=3D"= noreferrer" target=3D"_blank">https://mailman.open-bio.org/mailman/listinfo= /biopython</a><br> </blockquote></div> </blockquote></div> --000000000000a93bd5061387e35b-- --===============0757646579205830303== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Biopython mailing list - [email protected] https://mailman.open-bio.org/mailman/listinfo/biopython --===============0757646579205830303==--