[Biopython] error object is not callable, but callable() returns True

[Peter Cock]

On Mon, Dec 2, 2013 at 11:43 PM, Romelia Salomon
<romeliasalomon at gmail.com> wrote:
> Hi
>
> I am having problems using biopython on my laptop. I have Python version
> v2.6 and I recently installed biopython 1.53-1 using synaptic (I am using
> Ubuntu), but I can't get it to work right, I am having a problem running
> even the examples in the tutorial.
>
> When I try to use any of the command line wrappers I get an error saying
> the object is not callable, even though when I check that same object with
> callable() it does seem to be callable. For example:
>
> mycomputer$ python
> Python 2.6.5 (r265:79063, Sep 26 2013, 18:48:04)
> [GCC 4.4.3] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> from Bio.Align.Applications import MuscleCommandline
>>>> muscle_cline = MuscleCommandline(input="opuntia.fasta")
>>>> stdout, stderr = muscle_cline()
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
> TypeError: 'MuscleCommandline' object is not callable
>>>> callable(MuscleCommandline)
> True
>
> Thanks for your help!

Hi Romelia,

The simple answer is from the FAQ (in the current Biopython Tutorial),
http://biopython.org/DIST/docs/tutorial/Tutorial.html

"Why can’t I run command line tools directly from the application wrappers?
You need Biopython 1.55 or later. Alternatively, use the Python
subprocess module directly."

You are using Biopython 1.53 (which is now four years old), and it
doesn't have the __call__ method defined which made the class
callable in this way. Your investigation *almost* identified the
problem, but the key test you missed was:

callable(muscle_cline)

Unfortunately checking callable(MuscleCommandline) just confirmed
you can invoke MuscleCommandline(...) which you did to create
the object stored as muscle_cline.

So, I would suggest you uninstall the (very old) Ubunutu Biopython
(using 'sudo apt-get remove python-biopython') and then instead
install the current release from source. See:
http://biopython.org/wiki/Download#Ubuntu_or_Debian

Regards,

Peter