Re: [Biopython] Infernal output parser

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Hello Peter,

Thank you for your feedback. I confirmed with the developer of Infernal,
and both the tabular and plain text output format are stable. The code is
ready. I will open a pull request on GitHub.


Samuel

On Tue, Sep 17, 2024 at 12:18=E2=80=AFPM Peter Cock <p.j.a.cock@googlemail.=
com>
wrote:

> Hello Samuel,
>
> Looking back over old emails, someone once suggested including an Inferna=
l
> 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@g=
mail.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 adde=
d
>> 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">Hello Peter,=C2=A0<div><br></div><div>Thank you for your f=
eedback. I confirmed with the developer of Infernal, and both the tabular a=
nd plain text output format are stable. The code is ready. I will open a pu=
ll request on GitHub.=C2=A0</div><div><br></div><div><br></div><div>Samuel<=
/div></div><br><div class=3D"gmail_quote"><div dir=3D"ltr" class=3D"gmail_a=
ttr">On Tue, Sep 17, 2024 at 12:18=E2=80=AFPM Peter Cock &lt;<a href=3D"mai=
lto:[email protected]" target=3D"_blank">[email protected]<=
/a>&gt; wrote:<br></div><blockquote class=3D"gmail_quote" style=3D"margin:0=
px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><=
div dir=3D"ltr"><div>Hello Samuel,</div><div><br></div><div>Looking back ov=
er 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 hom=
e. I would probably focus on the tabular output as being simpler and more r=
obust to parse, but if the text output is stable that could be OK. I am war=
y given the history of the BLAST text output which changed lots over the ye=
ars.<br></div><br><div>Peter</div><div><br></div></div><br><div class=3D"gm=
ail_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]=
m" target=3D"_blank">[email protected]</a>&gt; wrote:<br></div><bl=
ockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-lef=
t:1px solid rgb(204,204,204);padding-left:1ex"><div dir=3D"ltr">Hello,=C2=
=A0<div><br></div><div>I am writing a BioPython parser for Infernal (cmsear=
ch and cmscan) standard text and tabular output. Would that be useful enoug=
h to be added to BioPython? Are there any specific aspects that I should kn=
ow before contributing to this?=C2=A0</div><div><br></div><div><br></div><d=
iv>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>
</blockquote></div>

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

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