Development purpose
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)
Deployment module
pip install pyproteins
Update pip module
TO DO
modules organization
container modules
Core
Frequently used container and functions. Downloading and parsing XML in a generic way. Two-level dictionnaries.
customCollection
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
sequence modules
msa
- Load alignemnt files
- Filter alignment
- Compute statistics
peptide
Fasta framed informations, like amino-acid types, domain boundaries and secondary structure states.
psipred
DEPRECATED
sequence alignment Modules
- nw_custom: the Needleman & Wunsch implementaion
- scoringFunctions : AA, AA/SS2, PWA
- scoringMatrix : Blosum62
utils modules
test Cecile
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