[Biopython] Using the Bio.SeqUtils.ProtParam module

Andrew Maher amaher at fas.harvard.edu
Fri Jul 23 15:22:32 UTC 2010


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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