add authorship to all modules

rhapsody/__init__.py

@@ -11,6 +11,12 @@
 
 __release__ = __version__
 
+__author__ = "Luca Ponzoni"
+__date__ = "December 2019"
+__maintainer__ = "Luca Ponzoni"
+__email__ = "[email protected]"
+__status__ = "Production"
+
 __all__ = []
 
 from . import utils

rhapsody/features/BLOSUM.py

@@ -5,6 +5,12 @@
 import numpy as np
 from Bio.SubsMat.MatrixInfo import blosum62
 
+__author__ = "Luca Ponzoni"
+__date__ = "December 2019"
+__maintainer__ = "Luca Ponzoni"
+__email__ = "[email protected]"
+__status__ = "Production"
+
 __all__ = ['BLOSUM_FEATS', 'calcBLOSUMfeatures']
 
 BLOSUM_FEATS = ['BLOSUM']

rhapsody/features/EVmutation.py

@@ -7,12 +7,11 @@
 from os.path import splitext, join, basename
 from prody import SETTINGS, LOGGER
 
-# extract precomputed EVmutation scores for given mutants
-# NB:
-# negative DeltaE_epist --> deleterious effect
-# DeltaE_epist == 0     --> neutral effect (wild-type)
-# positive DeltaE_epist --> neutral/benign effect
-
+__author__ = "Luca Ponzoni"
+__date__ = "December 2019"
+__maintainer__ = "Luca Ponzoni"
+__email__ = "[email protected]"
+__status__ = "Production"
 
 __all__ = ['EVMUT_FEATS', 'recoverEVmutFeatures']
 
@@ -35,6 +34,12 @@ def recoverEVmutFeatures(SAVs):
     LOGGER.timeit('_EVmut')
     LOGGER.info('Recovering EVmutation data...')
 
+    # extracts precomputed EVmutation scores for given mutants
+    # NB:
+    # negative DeltaE_epist --> deleterious effect
+    # DeltaE_epist == 0     --> neutral effect (wild-type)
+    # positive DeltaE_epist --> neutral/benign effect
+
     def find_matching_files(file_list, acc, pos):
         match_files = []
         for fname in [f for f in file_list if f.startswith(acc)]:

rhapsody/features/PDB.py

@@ -15,6 +15,11 @@
 from prody import reduceModel, sliceModel
 from prody import execDSSP, parseDSSP
 
+__author__ = "Luca Ponzoni"
+__date__ = "December 2019"
+__maintainer__ = "Luca Ponzoni"
+__email__ = "[email protected]"
+__status__ = "Production"
 
 __all__ = ['STR_FEATS', 'DYN_FEATS', 'PDB_FEATS',
            'PDBfeatures', 'calcPDBfeatures']

rhapsody/features/Pfam.py

@@ -9,6 +9,12 @@
 from prody import LOGGER
 from .Uniprot import UniprotMapping
 
+__author__ = "Luca Ponzoni"
+__date__ = "December 2019"
+__maintainer__ = "Luca Ponzoni"
+__email__ = "[email protected]"
+__status__ = "Production"
+
 __all__ = ['PFAM_FEATS', 'calcPfamFeatures']
 
 PFAM_FEATS = ['entropy', 'ranked_MI']

rhapsody/features/PolyPhen2.py

@@ -13,6 +13,12 @@
 from requests.packages.urllib3.util.retry import Retry
 from math import log
 
+__author__ = "Luca Ponzoni"
+__date__ = "December 2019"
+__maintainer__ = "Luca Ponzoni"
+__email__ = "[email protected]"
+__status__ = "Production"
+
 __all__ = ['PP2_FEATS', 'queryPolyPhen2', 'parsePolyPhen2output',
            'getSAVcoords', 'calcPolyPhen2features']
 

rhapsody/features/Uniprot.py

@@ -14,6 +14,12 @@
 from Bio.pairwise2 import format_alignment
 from Bio.SubsMat import MatrixInfo as matlist
 
+__author__ = "Luca Ponzoni"
+__date__ = "December 2019"
+__maintainer__ = "Luca Ponzoni"
+__email__ = "[email protected]"
+__status__ = "Production"
+
 __all__ = ['UniprotMapping', 'mapSAVs2PDB', 'seqScanning', 'printSAVlist']
 
 

rhapsody/features/__init__.py

@@ -4,6 +4,12 @@
 EVmutation precomputed data.
 """
 
+__author__ = "Luca Ponzoni"
+__date__ = "December 2019"
+__maintainer__ = "Luca Ponzoni"
+__email__ = "[email protected]"
+__status__ = "Production"
+
 __all__ = ['RHAPSODY_FEATS']
 
 from . import Uniprot

rhapsody/predict/__init__.py

@@ -5,6 +5,12 @@
 
 __all__ = []
 
+__author__ = "Luca Ponzoni"
+__date__ = "December 2019"
+__maintainer__ = "Luca Ponzoni"
+__email__ = "[email protected]"
+__status__ = "Production"
+
 from . import core
 from .core import *
 __all__.extend(core.__all__)

rhapsody/train/RFtraining.py

@@ -16,6 +16,11 @@
 from .figures import print_pred_distrib_figure, print_path_prob_figure
 from .figures import print_ROC_figure, print_feat_imp_figure
 
+__author__ = "Luca Ponzoni"
+__date__ = "December 2019"
+__maintainer__ = "Luca Ponzoni"
+__email__ = "[email protected]"
+__status__ = "Production"
 
 __all__ = ['calcScoreMetrics', 'calcClassMetrics', 'calcPathogenicityProbs',
            'RandomForestCV', 'trainRFclassifier',

rhapsody/train/__init__.py

@@ -3,6 +3,12 @@
 assess their accuracy.
 """
 
+__author__ = "Luca Ponzoni"
+__date__ = "December 2019"
+__maintainer__ = "Luca Ponzoni"
+__email__ = "[email protected]"
+__status__ = "Production"
+
 __all__ = []
 
 from . import RFtraining

rhapsody/train/figures.py

@@ -6,6 +6,12 @@
 import numpy as np
 from prody import LOGGER
 
+__author__ = "Luca Ponzoni"
+__date__ = "December 2019"
+__maintainer__ = "Luca Ponzoni"
+__email__ = "[email protected]"
+__status__ = "Production"
+
 __all__ = ['print_pred_distrib_figure', 'print_path_prob_figure',
            'print_ROC_figure', 'print_feat_imp_figure']
 

rhapsody/utils/__init__.py

@@ -3,6 +3,12 @@
 and for accessing installation settings and other parameters.
 """
 
+__author__ = "Luca Ponzoni"
+__date__ = "December 2019"
+__maintainer__ = "Luca Ponzoni"
+__email__ = "[email protected]"
+__status__ = "Production"
+
 __all__ = []
 
 from . import settings

rhapsody/utils/misc.py

@@ -12,6 +12,12 @@
 import prody as pd
 import rhapsody as rd
 
+__author__ = "Luca Ponzoni"
+__date__ = "December 2019"
+__maintainer__ = "Luca Ponzoni"
+__email__ = "[email protected]"
+__status__ = "Production"
+
 __all__ = ['DEFAULT_FEATSETS', 'initialSetup',
            'getDefaultTrainingDataset', 'getDefaultClassifiers',
            'importDefaultClassifier', 'delSettings', 'getSettings']

rhapsody/utils/settings.py

@@ -12,6 +12,12 @@
 import prody as pd
 import rhapsody as rd
 
+__author__ = "Luca Ponzoni"
+__date__ = "December 2019"
+__maintainer__ = "Luca Ponzoni"
+__email__ = "[email protected]"
+__status__ = "Production"
+
 __all__ = ['DEFAULT_FEATSETS', 'initialSetup',
            'getDefaultTrainingDataset', 'getDefaultClassifiers',
            'importDefaultClassifier', 'delSettings', 'getSettings']

setup.py

@@ -6,6 +6,12 @@
 from os import path
 from io import open
 
+__author__ = "Luca Ponzoni"
+__date__ = "December 2019"
+__maintainer__ = "Luca Ponzoni"
+__email__ = "[email protected]"
+__status__ = "Production"
+
 here = path.abspath(path.dirname(__file__))
 with open(path.join(here, 'VERSION'), encoding='utf-8') as f:
     version = f.read()

test/test-1/test-1.py

@@ -8,6 +8,13 @@
 sys.path.append('../../')
 import rhapsody as rd
 
+__author__ = "Luca Ponzoni"
+__date__ = "December 2019"
+__maintainer__ = "Luca Ponzoni"
+__email__ = "[email protected]"
+__status__ = "Production"
+
+
 # temporarily switch to new set of folders
 if not os.path.isdir('workspace'):
     os.mkdir('workspace')

test/test-2/test-2.py

@@ -7,6 +7,13 @@
 sys.path.append('../../')
 import rhapsody as rd
 
+__author__ = "Luca Ponzoni"
+__date__ = "December 2019"
+__maintainer__ = "Luca Ponzoni"
+__email__ = "[email protected]"
+__status__ = "Production"
+
+
 # temporarily switch to new set of folders
 if not os.path.isdir('workspace'):
     os.mkdir('workspace')