diff --git a/rhapsody/__init__.py b/rhapsody/__init__.py index eb5d235..c07620c 100644 --- a/rhapsody/__init__.py +++ b/rhapsody/__init__.py @@ -11,6 +11,12 @@ __release__ = __version__ +__author__ = "Luca Ponzoni" +__date__ = "December 2019" +__maintainer__ = "Luca Ponzoni" +__email__ = "lponzoni@pitt.edu" +__status__ = "Production" + __all__ = [] from . import utils diff --git a/rhapsody/features/BLOSUM.py b/rhapsody/features/BLOSUM.py index f432624..c3e4508 100644 --- a/rhapsody/features/BLOSUM.py +++ b/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__ = "lponzoni@pitt.edu" +__status__ = "Production" + __all__ = ['BLOSUM_FEATS', 'calcBLOSUMfeatures'] BLOSUM_FEATS = ['BLOSUM'] diff --git a/rhapsody/features/EVmutation.py b/rhapsody/features/EVmutation.py index 1a3f90f..8f52180 100644 --- a/rhapsody/features/EVmutation.py +++ b/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__ = "lponzoni@pitt.edu" +__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)]: diff --git a/rhapsody/features/PDB.py b/rhapsody/features/PDB.py index 4d8b27e..555a1a7 100644 --- a/rhapsody/features/PDB.py +++ b/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__ = "lponzoni@pitt.edu" +__status__ = "Production" __all__ = ['STR_FEATS', 'DYN_FEATS', 'PDB_FEATS', 'PDBfeatures', 'calcPDBfeatures'] diff --git a/rhapsody/features/Pfam.py b/rhapsody/features/Pfam.py index 57117e5..27548f3 100644 --- a/rhapsody/features/Pfam.py +++ b/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__ = "lponzoni@pitt.edu" +__status__ = "Production" + __all__ = ['PFAM_FEATS', 'calcPfamFeatures'] PFAM_FEATS = ['entropy', 'ranked_MI'] diff --git a/rhapsody/features/PolyPhen2.py b/rhapsody/features/PolyPhen2.py index b5ebf69..b9ce7b2 100644 --- a/rhapsody/features/PolyPhen2.py +++ b/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__ = "lponzoni@pitt.edu" +__status__ = "Production" + __all__ = ['PP2_FEATS', 'queryPolyPhen2', 'parsePolyPhen2output', 'getSAVcoords', 'calcPolyPhen2features'] diff --git a/rhapsody/features/Uniprot.py b/rhapsody/features/Uniprot.py index 83b8dc0..4c016cb 100644 --- a/rhapsody/features/Uniprot.py +++ b/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__ = "lponzoni@pitt.edu" +__status__ = "Production" + __all__ = ['UniprotMapping', 'mapSAVs2PDB', 'seqScanning', 'printSAVlist'] diff --git a/rhapsody/features/__init__.py b/rhapsody/features/__init__.py index af6cb8e..254bbbc 100644 --- a/rhapsody/features/__init__.py +++ b/rhapsody/features/__init__.py @@ -4,6 +4,12 @@ EVmutation precomputed data. """ +__author__ = "Luca Ponzoni" +__date__ = "December 2019" +__maintainer__ = "Luca Ponzoni" +__email__ = "lponzoni@pitt.edu" +__status__ = "Production" + __all__ = ['RHAPSODY_FEATS'] from . import Uniprot diff --git a/rhapsody/predict/__init__.py b/rhapsody/predict/__init__.py index a78b60e..c63e270 100644 --- a/rhapsody/predict/__init__.py +++ b/rhapsody/predict/__init__.py @@ -5,6 +5,12 @@ __all__ = [] +__author__ = "Luca Ponzoni" +__date__ = "December 2019" +__maintainer__ = "Luca Ponzoni" +__email__ = "lponzoni@pitt.edu" +__status__ = "Production" + from . import core from .core import * __all__.extend(core.__all__) diff --git a/rhapsody/train/RFtraining.py b/rhapsody/train/RFtraining.py index 4fde02d..42149dc 100644 --- a/rhapsody/train/RFtraining.py +++ b/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__ = "lponzoni@pitt.edu" +__status__ = "Production" __all__ = ['calcScoreMetrics', 'calcClassMetrics', 'calcPathogenicityProbs', 'RandomForestCV', 'trainRFclassifier', diff --git a/rhapsody/train/__init__.py b/rhapsody/train/__init__.py index fa8a85a..d7049c2 100644 --- a/rhapsody/train/__init__.py +++ b/rhapsody/train/__init__.py @@ -3,6 +3,12 @@ assess their accuracy. """ +__author__ = "Luca Ponzoni" +__date__ = "December 2019" +__maintainer__ = "Luca Ponzoni" +__email__ = "lponzoni@pitt.edu" +__status__ = "Production" + __all__ = [] from . import RFtraining diff --git a/rhapsody/train/figures.py b/rhapsody/train/figures.py index 4ea3ecc..988289f 100644 --- a/rhapsody/train/figures.py +++ b/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__ = "lponzoni@pitt.edu" +__status__ = "Production" + __all__ = ['print_pred_distrib_figure', 'print_path_prob_figure', 'print_ROC_figure', 'print_feat_imp_figure'] diff --git a/rhapsody/utils/__init__.py b/rhapsody/utils/__init__.py index e84fa6b..1554e0a 100644 --- a/rhapsody/utils/__init__.py +++ b/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__ = "lponzoni@pitt.edu" +__status__ = "Production" + __all__ = [] from . import settings diff --git a/rhapsody/utils/misc.py b/rhapsody/utils/misc.py index 3df3632..4c5f6f3 100644 --- a/rhapsody/utils/misc.py +++ b/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__ = "lponzoni@pitt.edu" +__status__ = "Production" + __all__ = ['DEFAULT_FEATSETS', 'initialSetup', 'getDefaultTrainingDataset', 'getDefaultClassifiers', 'importDefaultClassifier', 'delSettings', 'getSettings'] diff --git a/rhapsody/utils/settings.py b/rhapsody/utils/settings.py index 3df3632..4c5f6f3 100644 --- a/rhapsody/utils/settings.py +++ b/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__ = "lponzoni@pitt.edu" +__status__ = "Production" + __all__ = ['DEFAULT_FEATSETS', 'initialSetup', 'getDefaultTrainingDataset', 'getDefaultClassifiers', 'importDefaultClassifier', 'delSettings', 'getSettings'] diff --git a/setup.py b/setup.py index b208bbc..218bcf9 100644 --- a/setup.py +++ b/setup.py @@ -6,6 +6,12 @@ from os import path from io import open +__author__ = "Luca Ponzoni" +__date__ = "December 2019" +__maintainer__ = "Luca Ponzoni" +__email__ = "lponzoni@pitt.edu" +__status__ = "Production" + here = path.abspath(path.dirname(__file__)) with open(path.join(here, 'VERSION'), encoding='utf-8') as f: version = f.read() diff --git a/test/test-1/test-1.py b/test/test-1/test-1.py index f36b86a..b46c5e4 100644 --- a/test/test-1/test-1.py +++ b/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__ = "lponzoni@pitt.edu" +__status__ = "Production" + + # temporarily switch to new set of folders if not os.path.isdir('workspace'): os.mkdir('workspace') diff --git a/test/test-2/test-2.py b/test/test-2/test-2.py index 5f2c785..c0d11d7 100644 --- a/test/test-2/test-2.py +++ b/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__ = "lponzoni@pitt.edu" +__status__ = "Production" + + # temporarily switch to new set of folders if not os.path.isdir('workspace'): os.mkdir('workspace')