python-katlas 0.0.1__py3-none-any.whl

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Files changed (14) hide show
  1. katlas/__init__.py +1 -0
  2. katlas/_modidx.py +110 -0
  3. katlas/core.py +769 -0
  4. katlas/dl.py +355 -0
  5. katlas/feature.py +290 -0
  6. katlas/imports.py +7 -0
  7. katlas/plot.py +663 -0
  8. katlas/train.py +231 -0
  9. python_katlas-0.0.1.dist-info/LICENSE +201 -0
  10. python_katlas-0.0.1.dist-info/METADATA +402 -0
  11. python_katlas-0.0.1.dist-info/RECORD +14 -0
  12. python_katlas-0.0.1.dist-info/WHEEL +5 -0
  13. python_katlas-0.0.1.dist-info/entry_points.txt +2 -0
  14. python_katlas-0.0.1.dist-info/top_level.txt +1 -0
katlas/__init__.py ADDED
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+ __version__ = "0.0.1"
katlas/_modidx.py ADDED
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+ # Autogenerated by nbdev
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+
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+ d = { 'settings': { 'branch': 'main',
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+ 'doc_baseurl': '/katlas',
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+ 'doc_host': 'https://sky1ove.github.io',
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+ 'git_url': 'https://github.com/sky1ove/katlas',
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+ 'lib_path': 'katlas'},
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+ 'syms': { 'katlas.core': { 'katlas.core.CPTAC': ('core.html#cptac', 'katlas/core.py'),
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+ 'katlas.core.CPTAC._fetch_data': ('core.html#cptac._fetch_data', 'katlas/core.py'),
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+ 'katlas.core.CPTAC.get_id': ('core.html#cptac.get_id', 'katlas/core.py'),
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+ 'katlas.core.CPTAC.list_cancer': ('core.html#cptac.list_cancer', 'katlas/core.py'),
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+ 'katlas.core.Data': ('core.html#data', 'katlas/core.py'),
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+ 'katlas.core.Data.fetch_data': ('core.html#data.fetch_data', 'katlas/core.py'),
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+ 'katlas.core.Data.get_aa_info': ('core.html#data.get_aa_info', 'katlas/core.py'),
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+ 'katlas.core.Data.get_aa_morgan': ('core.html#data.get_aa_morgan', 'katlas/core.py'),
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+ 'katlas.core.Data.get_aa_rdkit': ('core.html#data.get_aa_rdkit', 'katlas/core.py'),
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+ 'katlas.core.Data.get_cddm': ('core.html#data.get_cddm', 'katlas/core.py'),
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+ 'katlas.core.Data.get_cddm_others': ('core.html#data.get_cddm_others', 'katlas/core.py'),
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+ 'katlas.core.Data.get_cddm_others_info': ('core.html#data.get_cddm_others_info', 'katlas/core.py'),
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+ 'katlas.core.Data.get_cddm_upper': ('core.html#data.get_cddm_upper', 'katlas/core.py'),
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+ 'katlas.core.Data.get_combine': ('core.html#data.get_combine', 'katlas/core.py'),
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+ 'katlas.core.Data.get_combine_site_psp_ochoa': ('core.html#data.get_combine_site_psp_ochoa', 'katlas/core.py'),
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+ 'katlas.core.Data.get_cptac_ensembl_site': ('core.html#data.get_cptac_ensembl_site', 'katlas/core.py'),
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+ 'katlas.core.Data.get_cptac_gene_site': ('core.html#data.get_cptac_gene_site', 'katlas/core.py'),
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+ 'katlas.core.Data.get_cptac_unique_site': ('core.html#data.get_cptac_unique_site', 'katlas/core.py'),
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+ 'katlas.core.Data.get_kinase_info': ('core.html#data.get_kinase_info', 'katlas/core.py'),
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+ 'katlas.core.Data.get_ks_dataset': ('core.html#data.get_ks_dataset', 'katlas/core.py'),
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+ 'katlas.core.Data.get_num_dict': ('core.html#data.get_num_dict', 'katlas/core.py'),
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+ 'katlas.core.Data.get_ochoa_site': ('core.html#data.get_ochoa_site', 'katlas/core.py'),
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+ 'katlas.core.Data.get_psp_human_site': ('core.html#data.get_psp_human_site', 'katlas/core.py'),
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+ 'katlas.core.Data.get_pspa_all_norm': ('core.html#data.get_pspa_all_norm', 'katlas/core.py'),
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+ 'katlas.core.Data.get_pspa_st_norm': ('core.html#data.get_pspa_st_norm', 'katlas/core.py'),
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+ 'katlas.core.Data.get_pspa_st_pct': ('core.html#data.get_pspa_st_pct', 'katlas/core.py'),
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+ 'katlas.core.Data.get_pspa_tyr_norm': ('core.html#data.get_pspa_tyr_norm', 'katlas/core.py'),
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+ 'katlas.core.Data.get_pspa_tyr_pct': ('core.html#data.get_pspa_tyr_pct', 'katlas/core.py'),
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+ 'katlas.core.STY2sty': ('core.html#sty2sty', 'katlas/core.py'),
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+ 'katlas.core.checker': ('core.html#checker', 'katlas/core.py'),
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+ 'katlas.core.convert_string': ('core.html#convert_string', 'katlas/core.py'),
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+ 'katlas.core.cut_seq': ('core.html#cut_seq', 'katlas/core.py'),
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+ 'katlas.core.extract_site_seq': ('core.html#extract_site_seq', 'katlas/core.py'),
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+ 'katlas.core.get_dict': ('core.html#get_dict', 'katlas/core.py'),
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+ 'katlas.core.get_freq': ('core.html#get_freq', 'katlas/core.py'),
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+ 'katlas.core.get_metaP': ('core.html#get_metap', 'katlas/core.py'),
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+ 'katlas.core.get_one_kinase': ('core.html#get_one_kinase', 'katlas/core.py'),
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+ 'katlas.core.get_pct': ('core.html#get_pct', 'katlas/core.py'),
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+ 'katlas.core.get_pct_df': ('core.html#get_pct_df', 'katlas/core.py'),
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+ 'katlas.core.get_ttest': ('core.html#get_ttest', 'katlas/core.py'),
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+ 'katlas.core.get_unique_site': ('core.html#get_unique_site', 'katlas/core.py'),
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+ 'katlas.core.multiply': ('core.html#multiply', 'katlas/core.py'),
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+ 'katlas.core.multiply.__init__': ('core.html#multiply.__init__', 'katlas/core.py'),
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+ 'katlas.core.multiply.func': ('core.html#multiply.func', 'katlas/core.py'),
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+ 'katlas.core.multiply_func': ('core.html#multiply_func', 'katlas/core.py'),
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+ 'katlas.core.predict_kinase': ('core.html#predict_kinase', 'katlas/core.py'),
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+ 'katlas.core.predict_kinase_df': ('core.html#predict_kinase_df', 'katlas/core.py'),
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+ 'katlas.core.query_gene': ('core.html#query_gene', 'katlas/core.py'),
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+ 'katlas.core.raw2norm': ('core.html#raw2norm', 'katlas/core.py'),
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+ 'katlas.core.sumup': ('core.html#sumup', 'katlas/core.py')},
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+ 'katlas.dl': { 'katlas.dl.CNN1D_1': ('dl.html#cnn1d_1', 'katlas/dl.py'),
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+ 'katlas.dl.CNN1D_1.__init__': ('dl.html#cnn1d_1.__init__', 'katlas/dl.py'),
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+ 'katlas.dl.CNN1D_1.forward': ('dl.html#cnn1d_1.forward', 'katlas/dl.py'),
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+ 'katlas.dl.CNN1D_2': ('dl.html#cnn1d_2', 'katlas/dl.py'),
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+ 'katlas.dl.CNN1D_2.__init__': ('dl.html#cnn1d_2.__init__', 'katlas/dl.py'),
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+ 'katlas.dl.CNN1D_2.forward': ('dl.html#cnn1d_2.forward', 'katlas/dl.py'),
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+ 'katlas.dl.GeneralDataset': ('dl.html#generaldataset', 'katlas/dl.py'),
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+ 'katlas.dl.GeneralDataset.__getitem__': ('dl.html#generaldataset.__getitem__', 'katlas/dl.py'),
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+ 'katlas.dl.GeneralDataset.__init__': ('dl.html#generaldataset.__init__', 'katlas/dl.py'),
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+ 'katlas.dl.GeneralDataset.__len__': ('dl.html#generaldataset.__len__', 'katlas/dl.py'),
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+ 'katlas.dl.MLP_1': ('dl.html#mlp_1', 'katlas/dl.py'),
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+ 'katlas.dl.conv_wn': ('dl.html#conv_wn', 'katlas/dl.py'),
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+ 'katlas.dl.get_sampler': ('dl.html#get_sampler', 'katlas/dl.py'),
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+ 'katlas.dl.init_weights': ('dl.html#init_weights', 'katlas/dl.py'),
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+ 'katlas.dl.lin_wn': ('dl.html#lin_wn', 'katlas/dl.py'),
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+ 'katlas.dl.predict_dl': ('dl.html#predict_dl', 'katlas/dl.py'),
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+ 'katlas.dl.seed_everything': ('dl.html#seed_everything', 'katlas/dl.py'),
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+ 'katlas.dl.train_dl': ('dl.html#train_dl', 'katlas/dl.py'),
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+ 'katlas.dl.train_dl_cv': ('dl.html#train_dl_cv', 'katlas/dl.py')},
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+ 'katlas.feature': { 'katlas.feature.get_esm': ('feature.html#get_esm', 'katlas/feature.py'),
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+ 'katlas.feature.get_morgan': ('feature.html#get_morgan', 'katlas/feature.py'),
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+ 'katlas.feature.get_rdkit': ('feature.html#get_rdkit', 'katlas/feature.py'),
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+ 'katlas.feature.get_t5': ('feature.html#get_t5', 'katlas/feature.py'),
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+ 'katlas.feature.get_t5_bfd': ('feature.html#get_t5_bfd', 'katlas/feature.py'),
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+ 'katlas.feature.preprocess': ('feature.html#preprocess', 'katlas/feature.py'),
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+ 'katlas.feature.reduce_feature': ('feature.html#reduce_feature', 'katlas/feature.py'),
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+ 'katlas.feature.remove_hi_corr': ('feature.html#remove_hi_corr', 'katlas/feature.py')},
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+ 'katlas.imports': {},
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+ 'katlas.plot': { 'katlas.plot.draw_corr': ('plot.html#draw_corr', 'katlas/plot.py'),
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+ 'katlas.plot.get_AUCDF': ('plot.html#get_aucdf', 'katlas/plot.py'),
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+ 'katlas.plot.get_color_dict': ('plot.html#get_color_dict', 'katlas/plot.py'),
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+ 'katlas.plot.get_logo': ('plot.html#get_logo', 'katlas/plot.py'),
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+ 'katlas.plot.get_logo2': ('plot.html#get_logo2', 'katlas/plot.py'),
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+ 'katlas.plot.logo_func': ('plot.html#logo_func', 'katlas/plot.py'),
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+ 'katlas.plot.plot_2d': ('plot.html#plot_2d', 'katlas/plot.py'),
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+ 'katlas.plot.plot_bar': ('plot.html#plot_bar', 'katlas/plot.py'),
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+ 'katlas.plot.plot_bokeh': ('plot.html#plot_bokeh', 'katlas/plot.py'),
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+ 'katlas.plot.plot_box': ('plot.html#plot_box', 'katlas/plot.py'),
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+ 'katlas.plot.plot_cluster': ('plot.html#plot_cluster', 'katlas/plot.py'),
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+ 'katlas.plot.plot_confusion_matrix': ('plot.html#plot_confusion_matrix', 'katlas/plot.py'),
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+ 'katlas.plot.plot_corr': ('plot.html#plot_corr', 'katlas/plot.py'),
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+ 'katlas.plot.plot_count': ('plot.html#plot_count', 'katlas/plot.py'),
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+ 'katlas.plot.plot_group_bar': ('plot.html#plot_group_bar', 'katlas/plot.py'),
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+ 'katlas.plot.plot_heatmap': ('plot.html#plot_heatmap', 'katlas/plot.py'),
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+ 'katlas.plot.plot_hist': ('plot.html#plot_hist', 'katlas/plot.py'),
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+ 'katlas.plot.plot_rank': ('plot.html#plot_rank', 'katlas/plot.py'),
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+ 'katlas.plot.set_sns': ('plot.html#set_sns', 'katlas/plot.py')},
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+ 'katlas.train': { 'katlas.train.get_splits': ('ml.html#get_splits', 'katlas/train.py'),
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+ 'katlas.train.predict_ml': ('ml.html#predict_ml', 'katlas/train.py'),
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+ 'katlas.train.score_each': ('ml.html#score_each', 'katlas/train.py'),
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+ 'katlas.train.split_data': ('ml.html#split_data', 'katlas/train.py'),
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+ 'katlas.train.train_ml': ('ml.html#train_ml', 'katlas/train.py'),
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+ 'katlas.train.train_ml_cv': ('ml.html#train_ml_cv', 'katlas/train.py')}}}