I am trying to learn Python for use in computational biology. I am using the
interesting book: "Computing for Biologists; Python Programming and Principles"
(by Ran Libeskind-Hadas and Eliot Bush). It has an interesting and useful set
of programming exercises at www.cs.hmc.edu/CFB. I am actually enjoying solving
(doing) the example problems. However, I find some of the instructions
non-functional for me. For example the import function does not work, nor
f=open("filename.txt"). I have saved files per instructions in the programming
exercise inside the Python34 folder (I am using Python 3.4 in Windows 7). But
use of the f=open() command produces an error message that the requested file
does not exist. I assume I have chosen a wrong location for the saved file
within that Python34 folder, but trial and error has not led to a successful
use of these functions. import simply leaves a blank line .. no suggestion
about the problem.
Asking questions in Google and Ask about where to save Python-related files
that can be used subsequently have not led to answers - just details about
structuring or formatting things to be written/saved/use of the \n at end of
each line, etc. Important details, but of no help. I am finding Python to be
very handy at many biologic things such as working with DNA strings, etc. but I
find the documentation and indexing for finding how to use many Python features
exasperating. I am writing to you based on a READ ME file in my Python folder
- generated when I installed Python.
FYI, I asked a few questions of one of the authors of the interesting book -
who politely replied he was too busy to answer right now - the book and
problems were meant for a class ... though neither the book nor problems say
so. The professor hopes to get around to issues of use by non-students
sometime - but not now.
Another feature I have come across so far that does not work is importation of
matplotlib. I copy computed results (that otherwise would go to your plotting
routine) then go to Excel and with manipulation produce a usable chart there -
but at a cost of time and energy.
Your Python tool has many intriguing features - but some of the most basic
functions do not work for me (even though many features do, e.g., import random
does work). The failure of these features - so far as I can tell - is because
of lack of description (for the general non-expert public) about where/how to
install various features. Perhaps I need to reinstall from the ground up???
If so, just what should I do? If there is a less drastic solution, can you
tell me about it?
Thank you for any help ... and if you could provide me a lead regarding WHERE
to ask subsequent questions I would be most grateful. Sometimes, Google or Ask
or a U Tube tutorial does a good job - but if one does not know the 'proper'
name or term for something, it often is frustrating or impossible to get an
answer. I have not heard about any comprehensive handbook for Python34 aimed
at one who wants to use Python for creating programs (functions) that work -
and is not an expert at back-room structure of files and folders.... have I
simply missed it? So far, I have not found a local Python expert to ask for
help. I am sure some are in the greater Seattle area where I live- but I don't
know how to find even one at this time.
Garry Crane
[email protected]
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