[Biopython] Problems with SeqFeature

[Kevin Bonham]

Hi Bastien,

Yeah, it looks like you're pulling from two different snippets and they're
not using the same conventions. When you're doing `from Bio.SeqFeature
import SeqFeature...`, you're overwriting what Python thinks `SeqFeature`
means from when you did `from Bio import SeqFeature`. And, as you say,
you're importing a bunch of stuff twice, which doesn't make much sense.

My recommendation would be to do:

    from Bio import SeqFeature as sf

    def myfun():
        spos = sf.BeforePosition(50);

        epos = sf.ExactPosition(100);

        l1 = sf.FeatureLocation(spos, epos, strand=+1)

        f1 = sf.SeqFeature(l1, strand=1, type="CDS", qualifiers={});

This way everything is nice and tidy, and you can see where those functions
came from in your code. Plus you have access to everything in
Bio.SeqFeature if you need it.

If you really only need those four things, and you want to reduce the
overhead a bit, you could do

    from Bio.SeqFeature import BeforePosition, ExactPosition,
FeatureLocation, SeqFeature

    ...

And then just use these unqualified. Hope this helps!

Kevin

PS I didn't actually try to run any of the above code and im typing on my
phone, so don't be mad if there's a syntax error somewhere :-)

On Mon, Nov 21, 2016, 1:03 PM Chevreux, Bastien <bastien.chevreux at dsm.com>
wrote:

> Hi all,
>
>
>
> I am basing my question on https://www.biostars.org/p/57549/ which gives
> a code snipped which shows on how to add SeqFeatures.
>
>
>
> Adapted, that code looks like this:
>
> ---
>
> from Bio import SeqFeature;
>
> spos = SeqFeature.BeforePosition(50);
>
> epos = SeqFeature.ExactPosition(100);
>
> from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation
>
> l1 = FeatureLocation(spos, epos, strand=+1)
>
> f1 = SeqFeature(l1, strand=1, type="CDS", qualifiers={});
>
> ---
>
>
>
> And it does work, no problem.
>
>
>
> However, I have some terrible issues with the above code: it imports
> SeqFeature twice. And I cannot write:
>
> ---
>
> from Bio import SeqFeature;
>
> from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation
>
> …
>
> ---
>
>
>
> as this will bomb.
>
>
>
> And therefore I cannot easily stick the above into a function without
> re-importing in the function every time I use the functionality. Like this:
>
>
>
> ---
>
> def myfun():
>
>     from Bio import SeqFeature;
>
>     spos = SeqFeature.BeforePosition(50);
>
>     epos = SeqFeature.ExactPosition(100);
>
>     from Bio.SeqFeature import SeqFeature, FeatureLocation,
> CompoundLocation
>
>     l 1 = FeatureLocation(spos, epos, strand=+1)
>
>     f1 = SeqFeature(l1, strand=1, type="CDS", qualifiers={});
>
> ---
>
>
>
> This seems so infinitely wrong to me. What’s the correct way to write a
> function like this:
>
>
>
> ---
>
> from … import …
>
> from … import …
>
>
>
> def myfun(x,y):
>
>     spos = SeqFeature.BeforePosition(x);
>
>     epos = SeqFeature.ExactPosition(y);
>
>     l 1 = FeatureLocation(spos, epos, strand=+1)
>
>     f1 = SeqFeature(l1, strand=1, type="CDS", qualifiers={});
>
>     return f1;
>
> ---
>
>
>
> Best,
>
>   Bastien
>
>
>
>
>
> --
> DSM Nutritional Products Microbia Inc | Bioinformatics
> 60 Westview Street | Lexington, MA 02421 | United States
> Phone +1 781 259 7613 | Fax +1 781 259 0615
>
>
>
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