Re: [Biopython] Infernal output parser

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Hello Samuel,

Looking back over old emails, someone once suggested including an Infernal
parser as part of Bio.SearchIO - I've not used the tool but that sounds a
sensible home. I would probably focus on the tabular output as being
simpler and more robust to parse, but if the text output is stable that
could be OK. I am wary given the history of the BLAST text output which
changed lots over the years.

Peter


On Mon, Sep 16, 2024 at 7:52=E2=80=AFPM Samuel Prince <samuel.ed.prince@gma=
il.com>
wrote:

> Hello,
>
> I am writing a BioPython parser for Infernal (cmsearch and cmscan)
> standard text and tabular output. Would that be useful enough to be added
> to BioPython? Are there any specific aspects that I should know before
> contributing to this?
>
>
> Thank you,
> Samuel
> _______________________________________________
> Biopython mailing list  -  [email protected]
> https://mailman.open-bio.org/mailman/listinfo/biopython
>

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<div dir=3D"ltr"><div>Hello Samuel,</div><div><br></div><div>Looking back o=
ver old emails, someone once suggested including an Infernal parser as part=
 of Bio.SearchIO - I&#39;ve not used the tool but that sounds a sensible ho=
me. I would probably focus on the tabular output as being simpler and more =
robust to parse, but if the text output is stable that could be OK. I am wa=
ry given the history of the BLAST text output which changed lots over the y=
ears.<br></div><br><div>Peter</div><div><br></div></div><br><div class=3D"g=
mail_quote"><div dir=3D"ltr" class=3D"gmail_attr">On Mon, Sep 16, 2024 at 7=
:52=E2=80=AFPM Samuel Prince &lt;<a href=3D"mailto:[email protected]=
om">[email protected]</a>&gt; wrote:<br></div><blockquote class=3D=
"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(2=
04,204,204);padding-left:1ex"><div dir=3D"ltr">Hello,=C2=A0<div><br></div><=
div>I am writing a BioPython parser for Infernal (cmsearch and cmscan) stan=
dard text and tabular output. Would that be useful enough to be added to Bi=
oPython? Are there any specific aspects that I should know before contribut=
ing to this?=C2=A0</div><div><br></div><div><br></div><div>Thank you,=C2=A0=
</div><div>Samuel=C2=A0<br></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>

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_______________________________________________
Biopython mailing list  -  [email protected]
https://mailman.open-bio.org/mailman/listinfo/biopython

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