[Biopython-dev] GSoC code+documentation review: PhyloXML for Biopython

Peter biopython at maubp.freeserve.co.uk
Sat Jul 4 16:39:13 UTC 2009

On Sat, Jul 4, 2009 at 5:28 PM, Eric Talevich<eric.talevich at gmail.com> wrote:
> On Sat, Jul 4, 2009 at 10:14 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:
>> The __repr__ thing isn't Biopython specific, its just what Python does. For
>> simple objects, eval(repr(obj)) should recreate the object. Consider:
>> >>> print phx.other
>> [Other(tag=alignment, namespace=http://example.org/align)]
>> That is odd to me. It looks like "other" is a list, containing an "Other"
>> object, but with a funny __repr__ - I would have expected it to look more
>> like this:
>> >>> print phx.other
>> [Other(tag="alignment", namespace="http://example.org/align")]
>> i.e. using the repr of what I have assumed are string arguments.
>> Peter
> Hi Peter,
> Thanks! Your interpretation of the example is correct. I'll change __repr__
> to check if the attribute is a string and, if so, escape and quote it.
> In the docs, I wrote that the representation is Biopython-style because by
> default, Python does something a little different for complex objects:
>>>> class Foo(object): pass
>>>> Foo()
> <__main__.Foo object at 0xb7cff22c>

Yes, that is the Python default for a user defined object.

> But I noticed that Seq and other Biopython objects give a nicer
> representation that actually works as a constructor, so I tried
> to match that.

I'd have to think of some more examples, but other Python
modules try to have eval(repr(obj)) work for their (simpler)

If you can do it without risking a really long string, this is a good
idea. You'll notice the Seq object repr actually uses a truncated
sequence for long sequences - you won't want to accidentally
get the whole thing printed at the python prompt! Likewise
doing repr() on a SeqRecord doesn't give you the full object.


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