git clone https://github.com/glaunay/pyproteins.git LOCAL_PATH_TO_REPO
Check for dependencies in LOCAL_PATH_TO_REPO/setup.py
sys.path.append(LOCAL_PATH_TO_REPO/src)
pip install pyproteins
TO DO
Frequently used container and functions. Downloading and parsing XML in a generic way. Two-level dictionnaries.
Managment of a collection of object which can be constructed from flat files (ex: uniprot).
- collectionPath: path to a directory of flat files
- constructor: object constructor
- indexer function to map filename and collection key
- Load alignemnt files
- Filter alignment
- Compute statistics
Fasta framed informations, like amino-acid types, domain boundaries and secondary structure states.
DEPRECATED
- nw_custom: the Needleman & Wunsch implementaion
- scoringFunctions : AA, AA/SS2, PWA
- scoringMatrix : Blosum62
test Cecile