[Biopython] Cannot make SeqFeature() comparable?

[Lenna Peterson]

re: Joshua's post about the key argument, here is an example of sorting
SeqFeatures by location start without (potentially error-prone) monkey
patching:

import operator
sorted_features = sorted([f1, f2],
key=operator.attrgetter("location.start"))

https://docs.python.org/2/library/operator.html#operator.attrgetter

Cheers,

Lenna

On Tue, Jan 31, 2017 at 9:31 AM, Chevreux, Bastien <bastien.chevreux at dsm.com
> wrote:

> > From: Joshua Klein [mailto:mobiusklein at gmail.com]
>
> > […] When assigning to the class itself, not the module, the new
>
> > comparator function is called
>
>
>
> Yay, that worked, learning something new every day. Thanks a million.
>
>
>
> Peter: the ultimate goal of that request was to be able to call sort() on
> features, with sometimes different and very custom sort criteria. Nothing
> which would fit BioPython really.
>
>
>
> 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
>
>
>
> *From:* Joshua Klein [mailto:mobiusklein at gmail.com]
> *Sent:* Tuesday, January 31, 2017 7:48 AM
> *To:* Peter Cock <p.j.a.cock at googlemail.com>
> *Cc:* Chevreux, Bastien <bastien.chevreux at dsm.com>;
> biopython at biopython.org
> *Subject:* Re: [Biopython] Cannot make SeqFeature() comparable?
>
>
>
> --- This mail has been sent from an external source ---
>
> The reason the original code snippet doesn’t seem to be working as
> expected is that the cmp1 function is assigned to the __lt__ attribute of
> the SeqFeature module, not the SeqFeature class, which is located at
> SeqFeature.SeqFeature. When assigning to the class itself, not the
> module, the new comparator function is called.
>
> This sort of patching works differently for old-style and new-style
> classes, having to do with how special methods are looked up. Old style
> classes look up special methods on the instance, new style classes look
> them up on the instance’s class.
>
> ​
>
>
>
> On Tue, Jan 31, 2017 at 4:07 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>
> Hi Bastien,
>
> I'm not immediately sure if "monkey patching" the class
> methods at run time like that would work in principle.
> If you insert a print into it, it does not seem to be invoked.
>
> It might be worth trying a modified Biopython, or an
> explicit subclass to narrow down where this breaks.
>
> Or more simply, can you just do the start position
> comparison explicitly if that's what you want to use?
>
> f1.location.start < f2.location.start
>
> Peter
>
>
>
> On Mon, Jan 30, 2017 at 11:05 PM, Chevreux, Bastien
> <bastien.chevreux at dsm.com> wrote:
> > Hi there,
> >
> >
> >
> > I have a problem making the SeqFeature() class comparable by providing a
> > __lt__ function. Consider the following:
> >
> >
> >
> > ------------------------------------------------------------------
> >
> > #!/usr/bin/env python3
> >
> >
> >
> > from Bio import SeqFeature
> >
> >
> >
> > def cmp1(this,other):
> >
> >     return int(this.location.start) < int(other.location.start);
> >
> >
> >
> > SeqFeature.__lt__=cmp1;
> >
> > f1 = SeqFeature.SeqFeature(SeqFeature.FeatureLocation(10, 200));
> >
> > f2 = SeqFeature.SeqFeature(SeqFeature.FeatureLocation(1000, 1200));
> >
> >
> >
> > if f1<f2:
> >
> >     print("f1<f2");
> >
> > else:
> >
> >     print("nope, f1>=f2");
> >
> > ------------------------------------------------------------------
> >
> >
> >
> > The code above runs with an error message:
> >
> >     if f1<f2:
> >
> > TypeError: unorderable types: SeqFeature() < SeqFeature()
> >
> >
> >
> > What I do not understand is that this should be the canonical recipe for
> > making any class comparable via LT operator. Compare to the following
> code
> > which runs without problems:
> >
> >
> >
> > ------------------------------------------------------------------
> >
> > #!/usr/bin/env python3
> >
> >
> >
> > class myclass():
> >
> >     def __init__(self, value):
> >
> >         self.bla=value;
> >
> >
> >
> > def cmp2(this,other):
> >
> >     return this.bla < other.bla;
> >
> >
> >
> > myclass.__lt__=cmp2;
> >
> > m1=myclass(1);
> >
> > m2=myclass(2);
> >
> >
> >
> > if m1<m2:
> >
> >     print("m1<m2");
> >
> > else:
> >
> >     print("nope, m1>=m2");
> >
> > ------------------------------------------------------------------
> >
> >
> >
> > What am I missing?
> >
> >
> >
> > 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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