Difference between revisions of "Python"

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=== What's that about? ===
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=== And now for something completely different... ===
  
Welcome to my personal [python1.html Python] homepage. At the moment you will only find some links to other sites, as I haven't had time to put together some stuff of general interest.
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Welcome to my personal [http://www.python.org Python] page. You will only find some links to other sites, as I haven't had time or energy to put together some stuff of general interest.
  
Python is a portable, object-oriented and last but not least easy-to-learn scripting language which can be used for everything from throwaway-scripting to [http://sketch.sourceforge.net complete applications] .
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Python is a portable, object-oriented and last but not least easy-to-learn scripting language which can be used for everything from throwaway-scripting to [http://www.skencil.org/ complete applications] .
  
Because it is quite easy to read and to understand, and because it is portable and especially because much stuff for processing [http://www.rcsb.org/pdb PDB-files] (containing information about molecular models (Proteins, RNA, organic and inorganic molecules) already existed, I had chosen Python as the implementation language for some data-parsing and conversion tools I desperately needed during and shortly after my [[Diploma|diploma]]-work.
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Because it is quite easy to read and to understand, and because it is portable and especially because much stuff for processing [http://www.rcsb.org/pdb/static.do?p=file_formats/index.jsp PDB-files] (containing information about molecular models (Proteins, RNA, organic and inorganic molecules) already existed, I had chosen Python as the implementation language for some data-parsing and conversion tools I desperately needed during and shortly after my [[Diploma|diploma]]-work.
  
 
More recently I have written some glue-logic for my [[Postdoc|Ph.D.]] work (macromolecular crystallography) which does more or less similar things as the GROMOS96-scripts: Input-generation and some logfile-parsing.
 
More recently I have written some glue-logic for my [[Postdoc|Ph.D.]] work (macromolecular crystallography) which does more or less similar things as the GROMOS96-scripts: Input-generation and some logfile-parsing.
  
And of course Python is essential, if you like [[Pymol]] , a molecular graphics program which uses it as its extension and scripting language.
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I got lucky in being paid to program in Python during my industry-career at [[Postdoc#Exelixis|Exelixis]],  [[Postdoc#BASF_Plant_Science_Company_GmbH|BASF Plant Science]] as well as [[Postdoc#BASF Business Services GmbH|BASF Business Services]].
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To be somehow usefull, here is the proof, that Python is good and Java and Perl are evil:
 +
<br />
 +
<syntaxhighlight lang="python">
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print "Hello world!"
 +
</syntaxhighlight>
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<br />
 +
Although this will have to be written as
 +
<br />
 +
<syntaxhighlight lang="python">
 +
print("Hello world!")
 +
</syntaxhighlight>
 +
<br />
 +
[http://www.python.org/download/releases/3.0/ from now on], still not bad compared to Java or Visual Basic.
 +
 
 +
If you still don't believe me, try this
 +
<br />
 +
<syntaxhighlight lang="python">
 +
from __future__ import braces
 +
</syntaxhighlight>
 +
<br />
 +
 
 +
And if you still don't believe me, read this
 +
 
 +
http://xkcd.com/353/
 +
 
 +
Visit my [https://github.com/MarcSaric GitHub] account for some Python code (most of which has been written by other people though).
 +
 
 +
=== Links ===
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* Some usefull extensions
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** [https://ipython.org/ iPython] -an enhanced interactive Python shell.
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** [http://matplotlib.sourceforge.net/index.html Matplotlib] -Reporting
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** [http://www.reportlab.org/ Reportlab] -Plotting
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* Python and Bioinformatics
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** [http://www.biopython.org Biopython] -Sequence manipulation et al. Like BioPerl
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** [https://github.com/pycogent/pycogent/ PyCogent] -A similar toolkit, but aimed at genomic biology
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** [http://code.google.com/p/pygr/ pygr] -Another package in the same direction,  
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** [https://github.com/bxlab/bx-python bx-python] -and yet another one
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** [http://bioinformatics.oxfordjournals.org/content/21/14/3164.full.pdf TAMO] -sequence motif analysis in Python

Latest revision as of 17:13, 25 January 2020

And now for something completely different...

Welcome to my personal Python page. You will only find some links to other sites, as I haven't had time or energy to put together some stuff of general interest.

Python is a portable, object-oriented and last but not least easy-to-learn scripting language which can be used for everything from throwaway-scripting to complete applications .

Because it is quite easy to read and to understand, and because it is portable and especially because much stuff for processing PDB-files (containing information about molecular models (Proteins, RNA, organic and inorganic molecules) already existed, I had chosen Python as the implementation language for some data-parsing and conversion tools I desperately needed during and shortly after my diploma-work.

More recently I have written some glue-logic for my Ph.D. work (macromolecular crystallography) which does more or less similar things as the GROMOS96-scripts: Input-generation and some logfile-parsing.

I got lucky in being paid to program in Python during my industry-career at Exelixis, BASF Plant Science as well as BASF Business Services.

To be somehow usefull, here is the proof, that Python is good and Java and Perl are evil:

print "Hello world!"


Although this will have to be written as

print("Hello world!")


from now on, still not bad compared to Java or Visual Basic.

If you still don't believe me, try this

from __future__ import braces


And if you still don't believe me, read this

http://xkcd.com/353/

Visit my GitHub account for some Python code (most of which has been written by other people though).

Links

  • Some usefull extensions
  • Python and Bioinformatics
    • Biopython -Sequence manipulation et al. Like BioPerl
    • PyCogent -A similar toolkit, but aimed at genomic biology
    • pygr -Another package in the same direction,
    • bx-python -and yet another one
    • TAMO -sequence motif analysis in Python