Re: Writing protein records in Swiss-Prot format

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Thanks for the explanation.

Note I have sometimes needed to *filter* a SwissProt
format file, and you can do this via SeqIO's index
get_raw functionality (grab the original raw record
as a string, and save it to a file as is). There's an
example of this in our Tutorial, see the section
"Getting the raw data for a record":

http://biopython.org/DIST/docs/tutorial/Tutorial.html

Peter

On Mon, Dec 25, 2017 at 4:05 PM, Adam Sj=C3=B8gren <[email protected]> wrot=
e:

> Peter writes:
>
> > I don't recall anyone asking about this, so there doesn't seem to be
> > much need for it. And perhaps because of this, no one has ever
> > written the code to do it. I've only ever needed to read these files.
> >
> > Why do you need Swiss aka SwissProt aka UniProt DAT format
> > output?
>
> I guess we should just use GenBank format.
>
> Traditionally (which in this case means: using BioPerl) we have been
> using SwissProt format when writing protein records, so I was just
> trying to do the same in BioPython, without any deeper thought going
> into it :-)
>
>
>   Thanks for the reply & merry christmas,
>
>     Adam
>
> --
>  "There are forty people in the world and five of them        Adam Sj=C3=
=B8gren
>   are hamburgers."                                       [email protected]=
k
>
> _______________________________________________
> Biopython-dev mailing list
> [email protected]
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>

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<div dir=3D"ltr">Thanks for the explanation.<div><br></div><div>Note I have=
 sometimes needed to *filter* a SwissProt</div><div>format file, and you ca=
n do this via SeqIO&#39;s index</div><div>get_raw functionality (grab the o=
riginal raw record</div><div>as a string, and save it to a file as is). The=
re&#39;s an</div><div>example of this in our Tutorial, see the section</div=
><div>&quot;Getting the raw data for a record&quot;:</div><div><br></div><d=
iv><a href=3D"http://biopython.org/DIST/docs/tutorial/Tutorial.html">http:/=
/biopython.org/DIST/docs/tutorial/Tutorial.html</a><br></div><div><br></div=
><div>Peter</div></div><div class=3D"gmail_extra"><br><div class=3D"gmail_q=
uote">On Mon, Dec 25, 2017 at 4:05 PM, Adam Sj=C3=B8gren <span dir=3D"ltr">=
&lt;<a href=3D"mailto:[email protected]" target=3D"_blank">[email protected]=
k</a>&gt;</span> wrote:<br><blockquote class=3D"gmail_quote" style=3D"margi=
n:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class=3D"">=
Peter writes:<br>
<br>
&gt; I don&#39;t recall anyone asking about this, so there doesn&#39;t seem=
 to be<br>
&gt; much need for it. And perhaps because of this, no one has ever<br>
&gt; written the code to do it. I&#39;ve only ever needed to read these fil=
es.<br>
&gt;<br>
&gt; Why do you need Swiss aka SwissProt aka UniProt DAT format<br>
&gt; output?<br>
<br>
</span>I guess we should just use GenBank format.<br>
<br>
Traditionally (which in this case means: using BioPerl) we have been<br>
using SwissProt format when writing protein records, so I was just<br>
trying to do the same in BioPython, without any deeper thought going<br>
into it :-)<br>
<br>
<br>
=C2=A0 Thanks for the reply &amp; merry christmas,<br>
<br>
=C2=A0 =C2=A0 Adam<br>
<span class=3D"HOEnZb"><font color=3D"#888888"><br>
--<br>
=C2=A0&quot;There are forty people in the world and five of them=C2=A0 =C2=
=A0 =C2=A0 =C2=A0 Adam Sj=C3=B8gren<br>
=C2=A0 are hamburgers.&quot;=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0<a href=3D"mailto:[email protected]">[email protected]<=
/a><br>
</font></span><div class=3D"HOEnZb"><div class=3D"h5"><br>
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