[Biopython] python advice needed

Csaba Kiss csaba.kiss at lanl.gov
Tue Apr 15 14:58:22 UTC 2014


Hi!
I need some advice how to get better in python. I have written a 
software package to analyze antibody deep sequencing data. This was my 
first experience with python and I am not a programmer. The end result 
works, however, if a professional coder looks at the scripts, it is 
obvious that it was written by an amateur. I am planning to re-write the 
code into a better format that is extendable and more user and coder 
friendly. At the moment the script only relies on biopython to get the 
sequences and quality values out of sff and fastq files, the rest is 
custom written. I would like to rely more on biopython and also perhaps 
extend biopython with new features.
The problem I am having is object oriented python and classes. I 
understand the concept of both, but it's completely different to 
actually use it. I would like to ask help from scientist who are in a 
similar situation, as myself. I am a molecular biologist with interest 
in coding, but little background. Do you have any good tutorials books 
about python classes and OOP? For example, when I learned python I found 
the Google python class, extremely valuable. I practically looked at the 
videos and solved the problems and that sent me on my way to python:
https://developers.google.com/edu/python/?csw=1

Any help would be appreciated:
Csaba

-- 
Best Regards:
Csaba Kiss PhD, MSc, BSc
TA-43, HRL-1, MS888
Los Alamos National Laboratory
Work: 1-505-667-9898
Cell: 1-505-920-5774




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