[Biopython] Using the Bio.SeqUtils.ProtParam module

[Andrew Maher]

Sorry, now I get this:

-bash-3.1$ python
Python 2.6.2 (r262:71600, Jul 27 2009, 17:05:24)
[GCC 4.1.2 20070626 (Red Hat 4.1.2-14)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import Bio.SeqUtils.ProtParam
>>>
ProtParam.ProteinAnalysis('VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPEASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
NameError: name 'ProtParam' is not defined
>>>

I wonder what's wrong...

On Fri, Jul 23, 2010 at 11:25 AM, João Rodrigues <anaryin at gmail.com> wrote:

> Hello Andrew,
>
> Try this: ProtParam.ProteinAnalysis(Sequence)
>
> Best,
>
> João [...] Rodrigues
> @ http://doeidoei.wordpress.org
>
>
>
> On Fri, Jul 23, 2010 at 5:22 PM, Andrew Maher <amaher at fas.harvard.edu>wrote:
>
>> I'm a beginner with python, and I'm having trouble with something
>> relatively
>> simple:
>>
>> I'm trying to find the isoelectric point of a protein with the
>> sequence:
>> VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPEASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC
>>
>> So, when I load python 2.6.2 with bipython v1.54 and then type in "from
>> Bio.SeqUtils import ProtParam" on one line and then "X =
>>
>> ProteinAnalysis("VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPEASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC")
>> on the next line, I get the following error message:
>>
>> NameError: name 'ProteinAnalysis' is not defined
>>
>> But, looking at the source code for ProtParam (
>>
>> http://biopython.org/DIST/docs/api/Bio.SeqUtils.ProtParam-pysrc.html#ProteinAnalysis
>> ),
>> isn't the ProteinAnalysis class clearly defined? What am I doing wrong?
>> _______________________________________________
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>>
>
>