[Biopython] python advice needed

[Kevin Rue]

Just adding a missing "but" in one of my sentences below:


On 16 April 2014 16:09, Kevin Rue <kevin.rue at ucdconnect.ie> wrote:

> Stephane,
>
> "I would first say that your code should first work"
>
> With all due respect, I would be careful how you phrased that, especially
> when talking to a beginner in programming. The way I understand it (not
> necessarily the way you meant it), this could be one of the worst advice I
> have heard.
> I would very much rather have a script that does not work but is well
> commented and documented (making it easier to debug), than a script copied
> from StackOverflow that works with obscure syntax and no comment to guide
> you in understanding it. Programming 1.0.1 in my opinion.
>
> To me, a script that is "pseudo-coded first", is much more likely to "work
> second" (i.e. first after the pseudo-code, excuse my play on words).
> Still in my humble opinion, creating a code that "works first" is one of
> the best way to write something that works fine in your particular little
> ultra-specific scenario. At best, it will need to be copy-pasted and edited
> for another scenario, more often you will start from scratch another script
> to "work first" in the second scenario.
>
> The PEP8 is a very good advice I forgot to mention. PyCharm is very useful
> in that regard as it checks the code for the PEP8 rules while it is typed.
>
> Regards,
> Kevin
>
>
> On 16 April 2014 13:38, Téletchéa Stéphane <stephane.teletchea at inserm.fr>wrote:
>
>> Le 15/04/2014 16:58, Csaba Kiss a écrit :
>>
>>  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
>>>
>>>
>> Dear Csaba,
>>
>> Being a bioinformatics teacher, I would first say that your code should
>> first work :-)
>>
>> Second, in order to get another version of your code, as mentioned
>> earlier, you should use
>> a git-like versioning control tool (git or any other, git tends to be
>> popular).
>>
>> Third, concerning python itself, I would recommend following the "PEP8"
>> recommandations:
>> http://legacy.python.org/dev/peps/pep-0008/
>>
>> (I also found this page while searching for PEP8 ->
>> http://docs.python-guide.org/en/latest/writing/style/)
>>
>> And last, since we are using biopython, check how biopython is
>> implemented (for example):
>> https://github.com/biopython/biopython/blob/master/Bio/
>> AlignIO/Interfaces.py
>>
>> Best,
>> Stéphane
>>
>> --
>> Equipe DSIMB - Dynamique des Structures et
>> des Interactions des Macromolécules Biologiques
>> INTS, INSERM-Paris-Diderot UMR_S 1134
>> 6 rue Alexandre Cabanel - 75739 Paris cedex 15 - France
>> Tél : +33 144 493 057
>> Fax : +33 147 347 431
>> http://www.dsimb.inserm.fr - http://www.steletch.org
>>
>>
>> _______________________________________________
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>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>
>
> --
> Kévin RUE-ALBRECHT
> Wellcome Trust Computational Infection Biology PhD Programme
> University College Dublin
> Ireland
> http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en
>



-- 
Kévin RUE-ALBRECHT
Wellcome Trust Computational Infection Biology PhD Programme
University College Dublin
Ireland
http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en