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