Θέλω να εγκαταστησω ενα προγραμμα βιοπληροφορικης στο φρέσκο ζουμπουντου 12.04 για να κανω πρόβλεψη καποια μοντέλα προτεϊνων για μια εργασία που κάνω για το σχολείο μου.
Το πρόγραμμα:
- Κώδικας: Επιλογή όλων
http://sourceforge.net/projects/poing/
Έχω εγκαταστησει τις απαραιτητες βιβλιοθήκες για αν τρέξει το πρόγραμμα σε python μέσω του synaptic, καλα μέχρι εδώ. Επειδή είμαι λίγο ψιλοάσχετος με τον πύθωνα δεν μπορώ να καταλάβω όταν λέει κάτω στις οδηγίες:
"Poing uses the standard Python mechanism for installation. Change to the root directory of the distribution archive, and type"
Λογικά θα πρέπει να αλλάξει σε κάποια συνδρομή στον δισκο μέσω τερμιναλ. Ειδάλως πέρνω την εξής απάντηση απο το τερματικό: (Χρησιμοποιώ έκδοση πύθωνα 3.2.3)
- Κώδικας: Επιλογή όλων
john@john-HP-G72-Notebook-PC:~/Desktop$ cd poing-1.0
john@john-HP-G72-Notebook-PC:~/Desktop/poing-1.0$ python setup.py install
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/poing
copying poing/common.py -> build/lib.linux-x86_64-2.7/poing
copying poing/model.py -> build/lib.linux-x86_64-2.7/poing
copying poing/__init__.py -> build/lib.linux-x86_64-2.7/poing
copying poing/gui.py -> build/lib.linux-x86_64-2.7/poing
copying poing/aminoAcidData.py -> build/lib.linux-x86_64-2.7/poing
copying poing/sourceProteinStructureNames.py -> build/lib.linux-x86_64-2.7/poing
copying poing/ooo.py -> build/lib.linux-x86_64-2.7/poing
copying poing/geometry.py -> build/lib.linux-x86_64-2.7/poing
copying poing/architecture.py -> build/lib.linux-x86_64-2.7/poing
copying poing/documentation.py -> build/lib.linux-x86_64-2.7/poing
copying poing/proteinMetrics.py -> build/lib.linux-x86_64-2.7/poing
copying poing/protein.py -> build/lib.linux-x86_64-2.7/poing
creating build/lib.linux-x86_64-2.7/poing/view
copying poing/view/common.py -> build/lib.linux-x86_64-2.7/poing/view
copying poing/view/__init__.py -> build/lib.linux-x86_64-2.7/poing/view
copying poing/view/cell.py -> build/lib.linux-x86_64-2.7/poing/view
running build_ext
building 'poing._protein' extension
swigging src/protein.i to src/protein_wrap.cpp
swig -python -c++ -python -o src/protein_wrap.cpp src/protein.i
unable to execute swig: No such file or directory
error: command 'swig' failed with exit status 1
Οι οδηγίες για εγκατασταση που έχει μέσα το πρόγραμμα:
Installing poing
Poing depends upon the following python libraries. Please install them before poing! Some are optional.
Biopython
numpy
PyOpenGL if you want to look at proteins being modelled
Poing uses the standard Python mechanism for installation. Change to the root directory of the distribution archive, and type:
- Κώδικας: Επιλογή όλων
python setup.py install
This will compile and install poing into the standard python place. Poing also relies upon two third party tools. maxcluster by Alex Herbert is used for getting the TM-score of modelled structure as compared to the native state. stride by Dmitrij Frishman is used for assigning secondary structure to proteins based upon their tertiary structure. Both are provided in the thirdParty directory. So you need to copy them somewhere they can be found for execution, for example:
- Κώδικας: Επιλογή όλων
cp thirdParty/maxcluster /usr/local/bin
cp thirdParty/stride/stride /usr/local/bin
rehash
The specifics depends on your system. But in the end, you should be able to type maxcluster and stride in a terminal and it can find those programs.
Running the examples
Check that poing is installed correctly by running the examples. Try this one just to check the basic modelling is working OK:
- Κώδικας: Επιλογή όλων
python examples/foldProtein.py
If you installed PyOpenGL, then this one should also work:
- Κώδικας: Επιλογή όλων
python examples/showProteinSynthesis.py
Exploring further
Clearly the examples are the best place to start in developing your own scripts. Poing is a library rather than a complete tool or program, so you have to write Python scripts to get it working. But it is very easy - look at the examples as a starting point.
Python library
To extend the examples, you'll need to refer to the Python library documentation. Almost everything you need to do to make use of poing's default functionality is accessed through Python.
C++ library
Hidden behind the Python library is a C++ library, which does the stuff which needs to be very fast. Sometimes you'll need to refer to the C++ library documentation, as some objects in the Python library are actually C++ objects in disguise, and you can access the C++ members directly from Python.
Developing poing
The source for both Python and C++ are supplied, please be adventurous and don't be afraid to get in there and change it.
The most likely thing you'll want to change in C++ is add new Effects. The C++ library documentation is what you'll need to get some idea of how to do this, but I suggest you start by copying a simple effect to get started.
If you edit the Python or the C++, then it is a simple matter of re-installing the module with:
- Κώδικας: Επιλογή όλων
python setup.py install
This will recompile the C++ code and reinstall. Next time you use poing it will be using your newly altered version.
