[Biopython-dev] SeqRecord comparison suggestion

[Peter Cock]

Resurrecting an old thread,

On Wed, Feb 5, 2014 at 6:15 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Tue, Feb 4, 2014 at 12:57 PM, Iddo Friedberg <idoerg at gmail.com> wrote:
>
>> Thanks!
>>
>> My initial thoughts are that seqrecord instances should not have an __eq__
>> operator. The equality operation here is somewhat meaningless when you
>> consider the number of parameters that can constitute a seqrecord,
>> especially when dealing with a genomic record or  a contig. This can lead
>> to unexpected behaviour.
>
> Indeed, which is one reason why we never defined __eq__ etc for the
> SeqRecord (how equal is equal? Same ID? Same sequence? Same
> annotions?).
>
> Therefore the SeqRecord gets the default Python object equality, which
> is are they the same object in memory?
>
> Peter

Since this discussion we have moved the Seq objects over to doing
string equality (with the alphabets only used to try to issue a warning).

Now, on to the SeqRecord. This now has a GitHub issue, 559

https://github.com/biopython/biopython/issues/559

We seem to have a consensus that there is no nice way to define
equality, and that the default id(...) based object equality is unhelpful.
This PR makes trying to compare a SeqRecord give an exception:

https://github.com/biopython/biopython/pull/560

It still needs some unit tests, but with Biopython 1.66 out, I think
we should make this change.

Any comments? Anything specific to the proposed implementation
can be done as a GitHub comment.

Peter