diff --git a/chrombpnet.egg-info/PKG-INFO b/chrombpnet.egg-info/PKG-INFO deleted file mode 100644 index 826a4896..00000000 --- a/chrombpnet.egg-info/PKG-INFO +++ /dev/null @@ -1,28 +0,0 @@ -Metadata-Version: 2.1 -Name: chrombpnet -Version: 0.1.5 -Summary: chrombpnet predicts chromatin accessibility from sequence -Download-URL: https://github.com/kundajelab/chrombpnet -Author-email: anusri @ stanford.edu -License: MIT -Requires-Python: >=3.8 -License-File: LICENSE -Requires-Dist: h5py>=2.10.0 -Requires-Dist: matplotlib>=3.3.1 -Requires-Dist: matplotlib-venn==0.11.6 -Requires-Dist: numpy==1.23.4 -Requires-Dist: pandas>=1.3.4 -Requires-Dist: pyfaidx==0.6.1 -Requires-Dist: scikit-learn>=1.1.2 -Requires-Dist: scipy>=1.4.1 -Requires-Dist: tensorflow==2.8.0 -Requires-Dist: tensorflow-estimator==2.8.0 -Requires-Dist: tensorflow-probability==0.15.0 -Requires-Dist: protobuf==3.20 -Requires-Dist: tqdm==4.48.2 -Requires-Dist: deepdish==0.3.7 -Requires-Dist: deeplift==0.6.13.0 -Requires-Dist: modisco==0.5.16.0 -Requires-Dist: modisco-lite==2.0.7 -Requires-Dist: weasyprint==52.5 -Requires-Dist: kundajelab-shap==1 diff --git a/chrombpnet.egg-info/SOURCES.txt b/chrombpnet.egg-info/SOURCES.txt deleted file mode 100644 index 1dd39e28..00000000 --- a/chrombpnet.egg-info/SOURCES.txt +++ /dev/null @@ -1,89 +0,0 @@ -LICENSE -MANIFEST.in -README.md -requirements.txt -setup.py -chrombpnet/CHROMBPNET.py -chrombpnet/__init__.py -chrombpnet/parsers.py -chrombpnet/pipelines.py -chrombpnet.egg-info/PKG-INFO -chrombpnet.egg-info/SOURCES.txt -chrombpnet.egg-info/dependency_links.txt -chrombpnet.egg-info/entry_points.txt -chrombpnet.egg-info/not-zip-safe -chrombpnet.egg-info/requires.txt -chrombpnet.egg-info/top_level.txt -chrombpnet/data/ATAC.ref.motifs.txt -chrombpnet/data/DNASE.ref.motifs.txt -chrombpnet/data/__init__.py -chrombpnet/data/motif_to_pwm.ATAC.tsv -chrombpnet/data/motif_to_pwm.DNASE.tsv -chrombpnet/data/motif_to_pwm.TF.tsv -chrombpnet/data/motifs.meme.txt -chrombpnet/evaluation/__init__.py -chrombpnet/evaluation/interpret/__init__.py -chrombpnet/evaluation/interpret/input_utils.py -chrombpnet/evaluation/interpret/interpret.py -chrombpnet/evaluation/interpret/shap_utils.py -chrombpnet/evaluation/invivo_footprints/__init__.py -chrombpnet/evaluation/invivo_footprints/run_tfmodisco.py -chrombpnet/evaluation/invivo_footprints/tf_modiscohits.py -chrombpnet/evaluation/make_bigwigs/__init__.py -chrombpnet/evaluation/make_bigwigs/bigwig_helper.py -chrombpnet/evaluation/make_bigwigs/importance_hdf5_to_bigwig.py -chrombpnet/evaluation/make_bigwigs/predict_to_bigwig.py -chrombpnet/evaluation/marginal_footprints/__init__.py -chrombpnet/evaluation/marginal_footprints/marginal_footprinting.py -chrombpnet/evaluation/modisco/__init__.py -chrombpnet/evaluation/modisco/convert_html_to_pdf.py -chrombpnet/evaluation/modisco/fetch_tomtom.py -chrombpnet/evaluation/modisco/run_modisco.py -chrombpnet/evaluation/modisco/visualize_motif_matches.py -chrombpnet/evaluation/variant_effect_prediction/__init__.py -chrombpnet/evaluation/variant_effect_prediction/snp_generator.py -chrombpnet/evaluation/variant_effect_prediction/snp_scoring.py -chrombpnet/evaluation/variant_effect_prediction/testing.py -chrombpnet/helpers/__init__.py -chrombpnet/helpers/generate_reports/__init__.py -chrombpnet/helpers/generate_reports/make_html.py -chrombpnet/helpers/generate_reports/make_html_bias.py -chrombpnet/helpers/hyperparameters/__init__.py -chrombpnet/helpers/hyperparameters/find_bias_hyperparams.py -chrombpnet/helpers/hyperparameters/find_chrombpnet_hyperparams.py -chrombpnet/helpers/hyperparameters/param_utils.py -chrombpnet/helpers/make_chr_splits/__init__.py -chrombpnet/helpers/make_chr_splits/splits.py -chrombpnet/helpers/make_gc_matched_negatives/__init__.py -chrombpnet/helpers/make_gc_matched_negatives/get_gc_content.py -chrombpnet/helpers/make_gc_matched_negatives/get_gc_matched_negatives.py -chrombpnet/helpers/make_gc_matched_negatives/get_genomewide_gc_buckets/__init__.py -chrombpnet/helpers/make_gc_matched_negatives/get_genomewide_gc_buckets/get_genomewide_gc_bins.py -chrombpnet/helpers/preprocessing/__init__.py -chrombpnet/helpers/preprocessing/auto_shift_detect.py -chrombpnet/helpers/preprocessing/reads_to_bigwig.py -chrombpnet/helpers/preprocessing/analysis/__init__.py -chrombpnet/helpers/preprocessing/analysis/build_pwm_from_bigwig.py -chrombpnet/training/__init__.py -chrombpnet/training/metrics.py -chrombpnet/training/predict.py -chrombpnet/training/train.py -chrombpnet/training/data_generators/__init__.py -chrombpnet/training/data_generators/batchgen_generator.py -chrombpnet/training/data_generators/initializers.py -chrombpnet/training/models/__init__.py -chrombpnet/training/models/bpnet_model.py -chrombpnet/training/models/chrombpnet_with_bias_model.py -chrombpnet/training/utils/__init__.py -chrombpnet/training/utils/argmanager.py -chrombpnet/training/utils/augment.py -chrombpnet/training/utils/callbacks.py -chrombpnet/training/utils/data_utils.py -chrombpnet/training/utils/losses.py -chrombpnet/training/utils/metrics_utils.py -chrombpnet/training/utils/one_hot.py -tests/full_workflow.sh -tests/genomewide_gc_bin_test.sh -tests/test_pred_to_bigwig.sh -workflows/train_bias_model.sh -workflows/train_chrombpnet_model.sh \ No newline at end of file diff --git a/chrombpnet.egg-info/dependency_links.txt b/chrombpnet.egg-info/dependency_links.txt deleted file mode 100644 index 8b137891..00000000 --- a/chrombpnet.egg-info/dependency_links.txt +++ /dev/null @@ -1 +0,0 @@ - diff --git a/chrombpnet.egg-info/entry_points.txt b/chrombpnet.egg-info/entry_points.txt deleted file mode 100644 index 26ec6379..00000000 --- a/chrombpnet.egg-info/entry_points.txt +++ /dev/null @@ -1,3 +0,0 @@ -[console_scripts] -chrombpnet = chrombpnet.CHROMBPNET:main -print_meme_motif_file = chrombpnet.data.__init__:print_meme_motif_file diff --git a/chrombpnet.egg-info/not-zip-safe b/chrombpnet.egg-info/not-zip-safe deleted file mode 100644 index 8b137891..00000000 --- a/chrombpnet.egg-info/not-zip-safe +++ /dev/null @@ -1 +0,0 @@ - diff --git a/chrombpnet.egg-info/requires.txt b/chrombpnet.egg-info/requires.txt deleted file mode 100644 index 2656630a..00000000 --- a/chrombpnet.egg-info/requires.txt +++ /dev/null @@ -1,19 +0,0 @@ -h5py>=2.10.0 -matplotlib>=3.3.1 -matplotlib-venn==0.11.6 -numpy==1.23.4 -pandas>=1.3.4 -pyfaidx==0.6.1 -scikit-learn>=1.1.2 -scipy>=1.4.1 -tensorflow==2.8.0 -tensorflow-estimator==2.8.0 -tensorflow-probability==0.15.0 -protobuf==3.20 -tqdm==4.48.2 -deepdish==0.3.7 -deeplift==0.6.13.0 -modisco==0.5.16.0 -modisco-lite==2.0.7 -weasyprint==52.5 -kundajelab-shap==1 diff --git a/chrombpnet.egg-info/top_level.txt b/chrombpnet.egg-info/top_level.txt deleted file mode 100644 index a55b8bb4..00000000 --- a/chrombpnet.egg-info/top_level.txt +++ /dev/null @@ -1 +0,0 @@ -chrombpnet diff --git a/chrombpnet/evaluation/hit_caller/README.save b/chrombpnet/evaluation/hit_caller/README.save deleted file mode 100644 index 336bc7b9..00000000 --- a/chrombpnet/evaluation/hit_caller/README.save +++ /dev/null @@ -1,8 +0,0 @@ - - - - - - -c - diff --git a/chrombpnet/evaluation/temp.txt b/chrombpnet/evaluation/temp.txt deleted file mode 100644 index a9d3f6f7..00000000 --- a/chrombpnet/evaluation/temp.txt +++ /dev/null @@ -1,2 +0,0 @@ -a b c -d e f diff --git a/dist/chrombpnet-0.1.5-py3-none-any.whl b/dist/chrombpnet-0.1.5-py3-none-any.whl deleted file mode 100644 index 74222cad..00000000 Binary files a/dist/chrombpnet-0.1.5-py3-none-any.whl and /dev/null differ diff --git a/dist/chrombpnet-0.1.5.tar.gz b/dist/chrombpnet-0.1.5.tar.gz deleted file mode 100644 index 6ddc3138..00000000 Binary files a/dist/chrombpnet-0.1.5.tar.gz and /dev/null differ diff --git a/test_bb.bed b/test_bb.bed deleted file mode 100644 index 93c1cfba..00000000 --- a/test_bb.bed +++ /dev/null @@ -1,2 +0,0 @@ -chr15 82849368 82850431 Peak_144929 497 . 2.47806 49.77871 47.75513 944 -chr21 29953189 29953384 Peak_193060 293 . 3.56959 29.30855 27.40983 92