do approp filtering for contribs and bw write fix

chrombpnet.egg-info/PKG-INFO

@@ -0,0 +1,28 @@
+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

chrombpnet.egg-info/SOURCES.txt

@@ -0,0 +1,89 @@
+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

chrombpnet.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

chrombpnet.egg-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+chrombpnet = chrombpnet.CHROMBPNET:main
+print_meme_motif_file = chrombpnet.data.__init__:print_meme_motif_file

chrombpnet.egg-info/not-zip-safe

@@ -0,0 +1 @@
+

chrombpnet.egg-info/requires.txt

@@ -0,0 +1,19 @@
+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

chrombpnet.egg-info/top_level.txt

@@ -0,0 +1 @@
+chrombpnet

chrombpnet/CHROMBPNET.py

@@ -64,12 +64,14 @@ def main():
 			args_copy = copy.deepcopy(args)
 			args_copy.hdf5 = args_copy.output_prefix + ".counts_scores.h5"
 			args_copy.output_prefix = args.output_prefix + ".counts_scores"
-
+			args_copy.regions =  args.output_prefix + ".interpreted_regions.bed"
+
 			importance_hdf5_to_bigwig.main(args_copy)
 		if "profile" in  args.profile_or_counts:
 			args_copy = copy.deepcopy(args)
 			args_copy.hdf5 = args_copy.output_prefix + ".profile_scores.h5"
 			args_copy.output_prefix = args.output_prefix + ".profile_scores"
+			args_copy.regions =  args.output_prefix + ".interpreted_regions.bed"
 
 			importance_hdf5_to_bigwig.main(args_copy)
 

chrombpnet/evaluation/hit_caller/README.save

@@ -0,0 +1,8 @@
+
+
+
+
+
+
+c
+

chrombpnet/evaluation/interpret/interpret.py

@@ -127,7 +127,7 @@ def main(args):
     seqs, peaks_used = input_utils.get_seq(regions_df, genome, inputlen)
     genome.close()
 
-    regions_df[peaks_used].to_csv("{}.interpreted_regions.bed".format(args.output_prefix), header=False, sep='\t')
+    regions_df[peaks_used].to_csv("{}.interpreted_regions.bed".format(args.output_prefix), header=False, index=False, sep='\t')
 
     interpret(model, seqs, args.output_prefix, args.profile_or_counts)
 

chrombpnet/evaluation/make_bigwigs/bigwig_helper.py

@@ -38,7 +38,10 @@ def get_regions(regions_file, seqlen, regions_used=None):
 
     regions = pd.read_csv(regions_file,sep='\t',header=None)
     #print(regions)
-    regions = [[x[0], int(x[1])+int(x[9])-seqlen//2, int(x[1])+int(x[9])+seqlen//2, int(x[1])+int(x[9])] for x in np.array(regions.values)[regions_used]]
+    if regions_used:
+        regions = [[x[0], int(x[1])+int(x[9])-seqlen//2, int(x[1])+int(x[9])+seqlen//2, int(x[1])+int(x[9])] for x in np.array(regions.values)[regions_used]]
+    else:
+        regions = [[x[0], int(x[1])+int(x[9])-seqlen//2, int(x[1])+int(x[9])+seqlen//2, int(x[1])+int(x[9])] for x in np.array(regions.values)]
 
     return regions
 

chrombpnet/evaluation/make_bigwigs/importance_hdf5_to_bigwig.py

@@ -28,6 +28,7 @@ def main(args):
 
 	gs = bigwig_helper.read_chrom_sizes(args.chrom_sizes)
 	regions = bigwig_helper.get_regions(args.regions, SEQLEN)
+	assert(d.shape[0] == len(regions))
 
 	bigwig_helper.write_bigwig(d.sum(1), 
                            regions, 

chrombpnet/evaluation/temp.txt

@@ -0,0 +1,2 @@
+a	b	c
+d	e	f

setup.py

@@ -13,7 +13,7 @@
     'include_package_data': True,
     'description': 'chrombpnet predicts chromatin accessibility from sequence',
     'download_url': 'https://github.com/kundajelab/chrombpnet',
-    'version': '0.1.5',
+    'version': '0.1.6',
     'packages': find_packages(),
     'python_requires': '>=3.8',
     'install_requires': install_requires,

test_bb.bed

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+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