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Added documentation

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basvandenberg committed Oct 3, 2013
1 parent 9d9f8bc commit e47bef7d78d605fa450affe446d0bc4556199456
Showing with 24 additions and 33 deletions.
  1. +24 −33 README.md
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@@ -6,41 +6,17 @@ The spice package can be used for calculating sequence-based protein features,
visualizing the obtained features, and training and testing of protein
classifiers using these features.
This featext.py module can be used for sequence-based protein feature
extraction. it uses the featmat.py module to manage the labeled feature
matrix, an m x n matrix for m proteins and n features, and the dataset.py
module to manage the set of proteins and their corresponding labels.
featext.py
----------
This module can be used for sequence-based protein feature extraction.
The classification.py module is a layer on top of scikit-learn that can be used
to construct protein classifiers and the classify.py module can be used to test
new protein sequences on an allready trained classifier.
featmat.py
----------
This module manages the labeled feature matrix. An m x n matrix for m proteins
and n features that can be build using the featext module.
dataset.py
----------
This module manages the set of proteins and their corresponding labels.
classification.py
-----------------
A layer on top of scikit-learn that can be used to construct protein
classifiers.
classify.py
-----------
This module can be used to test new protein sequences on an allready trained
classifier.
project\_management.py
---------------------
This module is used by the SPiCE website to manage user projects.
The project\_management.py module is used by the SPiCE website to manage user
projects.
Dependencies
@@ -65,3 +41,18 @@ Install
On linux systems, the sofware can be installed using:
sudo python setup.py install
Usage
=====
The software can be using the import statement, for example:
from spice import featext
Four command-line tools are also provided:
- featext
- classification
- classify

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