Index

A

activate() (in module baskerville.layers) adaptive_clip_grad() (in module baskerville.trainer) add_exon() (baskerville.gene.Gene method)

add_gene() (baskerville.snps.GeneSNPCluster method) add_snp() (baskerville.snps.SNPCluster method) annotate_unmap() (in module baskerville.data)

B

baskerville module baskerville.bed module baskerville.blocks module baskerville.data module baskerville.dataset module baskerville.dna module baskerville.gene module baskerville.helpers module baskerville.helpers.gcs_utils module baskerville.helpers.h5_baskerville_utils module baskerville.helpers.h5_utils module baskerville.helpers.tensorrt_helpers module baskerville.helpers.trt_optimized_model module baskerville.helpers.utils module baskerville.layers module baskerville.metrics module baskerville.scripts module baskerville.scripts.hound_data module baskerville.scripts.hound_data_align module baskerville.scripts.hound_data_read module baskerville.scripts.hound_data_write module baskerville.scripts.hound_eval module

baskerville.scripts.hound_eval_spec module baskerville.scripts.hound_ism_bed module baskerville.scripts.hound_ism_snp module baskerville.scripts.hound_predbed module baskerville.scripts.hound_snp module baskerville.scripts.hound_snpgene module baskerville.scripts.hound_train module baskerville.seqnn module baskerville.snps module baskerville.trainer module baskerville.vcf module batches_per_epoch() (baskerville.dataset.SeqDataset method) bedtool_exon() (baskerville.gene.Transcriptome method) bedtool_span() (baskerville.gene.Transcriptome method) bigwig_open() (in module baskerville.scripts.hound_predbed) bigwig_write() (in module baskerville.scripts.hound_predbed) break_large_contigs() (in module baskerville.data) (in module baskerville.scripts.hound_data_align) build() (baskerville.helpers.tensorrt_helpers.ModelOptimizer method) (baskerville.layers.GlobalContext method) (baskerville.layers.Scale method) (baskerville.layers.SoftmaxPool1D method) (baskerville.layers.SqueezeExcite method) (baskerville.layers.WheezeExcite method) build_block() (baskerville.seqnn.SeqNN method) build_embed() (baskerville.seqnn.SeqNN method) build_ensemble() (baskerville.seqnn.SeqNN method) build_func() (baskerville.helpers.tensorrt_helpers.ModelOptimizer method) build_model() (baskerville.seqnn.SeqNN method) build_sad() (baskerville.seqnn.SeqNN method) build_slice() (baskerville.seqnn.SeqNN method)

C

call() (baskerville.layers.CenterAverage method) (baskerville.layers.CenterSlice method) (baskerville.layers.ConcatDist2D method) (baskerville.layers.ConcatPosition method) (baskerville.layers.EnsembleReverseComplement method) (baskerville.layers.EnsembleShift method) (baskerville.layers.FactorInverse method) (baskerville.layers.GlobalContext method) (baskerville.layers.LengthAverage method) (baskerville.layers.MultiheadAttention method) (baskerville.layers.OneToTwo method) (baskerville.layers.Scale method) (baskerville.layers.SoftmaxPool1D method) (baskerville.layers.Softplus method) (baskerville.layers.SqueezeExcite method) (baskerville.layers.StochasticReverseComplement method) (baskerville.layers.StochasticShift method) (baskerville.layers.SwitchReverse method) (baskerville.layers.SwitchReverseTriu method) (baskerville.layers.Symmetrize2D method) (baskerville.layers.UpperTri method) (baskerville.layers.WheezeExcite method) cap_allele() (in module baskerville.vcf) center_average() (in module baskerville.blocks) center_slice() (in module baskerville.blocks) CenterAverage (class in baskerville.layers) CenterSlice (class in baskerville.layers) chr (baskerville.data.Contig attribute) (baskerville.data.ModelSeq attribute) (baskerville.scripts.hound_data_align.GraphSeq attribute) close() (baskerville.scripts.hound_data_read.CovFace method)

cluster_genes() (in module baskerville.snps) cluster_snps() (in module baskerville.snps) collect_h5() (in module baskerville.helpers.h5_baskerville_utils) (in module baskerville.helpers.h5_utils) collect_h5_borzoi() (in module baskerville.helpers.h5_utils) compile() (baskerville.trainer.Trainer method) compute_norm() (in module baskerville.trainer) compute_scores() (in module baskerville.snps) compute_stats() (baskerville.dataset.SeqDataset method) concat_dist_2d() (in module baskerville.blocks) concat_position() (in module baskerville.blocks) ConcatDist2D (class in baskerville.layers) ConcatPosition (class in baskerville.layers) connect_contigs() (in module baskerville.scripts.hound_data_align) Contig (class in baskerville.data) contig_sequences() (in module baskerville.data) contig_stats_genome() (in module baskerville.scripts.hound_data_align) conv_block() (in module baskerville.blocks) conv_block_2d() (in module baskerville.blocks) conv_dna() (in module baskerville.blocks) conv_nac() (in module baskerville.blocks) conv_next() (in module baskerville.blocks) conv_tower() (in module baskerville.blocks) conv_tower_nac() (in module baskerville.blocks) conv_tower_v1() (in module baskerville.blocks) convert() (baskerville.helpers.tensorrt_helpers.ModelOptimizer method) convnext_tower() (in module baskerville.blocks) CovFace (class in baskerville.scripts.hound_data_read) cropping_2d() (in module baskerville.blocks) curate_peaks() (in module baskerville.scripts.hound_data) Cyclical1LearningRate (class in baskerville.trainer)

D

delimit() (baskerville.snps.GeneSNPCluster method) (baskerville.snps.SNPCluster method) dense_block() (in module baskerville.blocks) dense_nac() (in module baskerville.blocks) dilated_dense() (in module baskerville.blocks) dilated_residual() (in module baskerville.blocks) dilated_residual_2d() (in module baskerville.blocks) dilated_residual_nac() (in module baskerville.blocks) distribute() (baskerville.dataset.SeqDataset method) divide_components_folds() (in module baskerville.scripts.hound_data_align) divide_components_pct() (in module baskerville.scripts.hound_data_align)

divide_contigs_chr() (in module baskerville.scripts.hound_data) divide_contigs_folds() (in module baskerville.scripts.hound_data) divide_contigs_pct() (in module baskerville.scripts.hound_data) dna_1hot() (in module baskerville.dna) dna_1hot_index() (in module baskerville.dna) dna_length_1hot() (in module baskerville.vcf) dna_rc() (in module baskerville.dna) downcast() (baskerville.seqnn.SeqNN method) download_folder_from_gcs() (in module baskerville.helpers.gcs_utils) download_from_gcs() (in module baskerville.helpers.gcs_utils) download_rename_inputs() (in module baskerville.helpers.gcs_utils)

E

EarlyStoppingMin (class in baskerville.trainer) end (baskerville.data.Contig attribute) (baskerville.data.ModelSeq attribute) (baskerville.scripts.hound_data_align.GraphSeq attribute)

EnsembleReverseComplement (class in baskerville.layers) EnsembleShift (class in baskerville.layers) evaluate() (baskerville.seqnn.SeqNN method) exec_par() (in module baskerville.helpers.utils)

F

factor_inverse() (in module baskerville.blocks) FactorInverse (class in baskerville.layers) feature_bytes() (in module baskerville.scripts.hound_data_write) feature_floats() (in module baskerville.scripts.hound_data_write) fetch_dna() (in module baskerville.scripts.hound_data_write)

file_to_records() (in module baskerville.dataset) final() (in module baskerville.blocks) fit2() (baskerville.trainer.Trainer method) fit_keras() (baskerville.trainer.Trainer method) fit_tape() (baskerville.trainer.Trainer method) flip_alleles() (baskerville.vcf.SNP method)

G

gcs_file_exist() (in module baskerville.helpers.gcs_utils) gcs_join() (in module baskerville.helpers.gcs_utils) Gene (class in baskerville.gene) generate_parser() (baskerville.dataset.SeqDataset method) GeneSNPCluster (class in baskerville.snps) genome (baskerville.data.Contig attribute) (baskerville.data.ModelSeq attribute) (baskerville.scripts.hound_data_align.GraphSeq attribute) GenomicInterval (class in baskerville.gene) get_1hots() (baskerville.snps.SNPCluster method) get_alleles() (baskerville.vcf.SNP method) get_bn_layer() (baskerville.seqnn.SeqNN method) get_config() (baskerville.layers.CenterAverage method) (baskerville.layers.CenterSlice method) (baskerville.layers.ConcatPosition method) (baskerville.layers.EnsembleShift method) (baskerville.layers.FactorInverse method) (baskerville.layers.MultiheadAttention method) (baskerville.layers.OneToTwo method) (baskerville.layers.Scale method) (baskerville.layers.SoftmaxPool1D method) (baskerville.layers.Softplus method) (baskerville.layers.SqueezeExcite method) (baskerville.layers.StochasticShift method) (baskerville.layers.SwitchReverse method) (baskerville.layers.SwitchReverseTriu method) (baskerville.layers.UpperTri method) (baskerville.layers.WheezeExcite method) (baskerville.trainer.Cyclical1LearningRate method) (baskerville.trainer.WarmUp method)

get_conv_layer() (baskerville.seqnn.SeqNN method) get_conv_weights() (baskerville.seqnn.SeqNN method) get_dense_layer() (baskerville.seqnn.SeqNN method) get_exons() (baskerville.gene.Gene method) get_filename_in_dir() (in module baskerville.helpers.gcs_utils) global_context() (in module baskerville.blocks) GlobalContext (class in baskerville.layers) gradients() (baskerville.seqnn.SeqNN method) gradients_func() (baskerville.seqnn.SeqNN method) gradients_func_orig() (baskerville.seqnn.SeqNN method) gradients_orig() (baskerville.seqnn.SeqNN method) GraphSeq (class in baskerville.scripts.hound_data_align) gtf_kv() (in module baskerville.gene)

H

hot1_augment() (in module baskerville.dna) hot1_delete() (in module baskerville.dna) hot1_dna() (in module baskerville.dna)

hot1_get() (in module baskerville.dna) hot1_insert() (in module baskerville.dna) hot1_rc() (in module baskerville.dna) hot1_set() (in module baskerville.dna)

I

indel_size() (baskerville.vcf.SNP method) initialize_output_h5() (in module baskerville.snps) interp_nan() (in module baskerville.scripts.hound_data_read) interpolate_pr_auc() (baskerville.metrics.SeqAUC method)

intersect_contigs_nets() (in module baskerville.scripts.hound_data_align) intersect_seqs_snps() (in module baskerville.vcf) intersect_snps_seqs() (in module baskerville.vcf) is_gcs_path() (in module baskerville.helpers.gcs_utils)

L

label (baskerville.data.ModelSeq attribute) LengthAverage (class in baskerville.layers) limit_contigs() (in module baskerville.scripts.hound_data)

load_chromosomes() (in module baskerville.data) load_extra_options() (in module baskerville.helpers.utils) load_model() (baskerville.helpers.trt_optimized_model.OptimizedModel method) longest_alt() (baskerville.vcf.SNP method)

M

main() (in module baskerville.helpers.h5_baskerville_utils) (in module baskerville.helpers.tensorrt_helpers) (in module baskerville.scripts.hound_data) (in module baskerville.scripts.hound_data_align) (in module baskerville.scripts.hound_data_read) (in module baskerville.scripts.hound_data_write) (in module baskerville.scripts.hound_eval) (in module baskerville.scripts.hound_eval_spec) (in module baskerville.scripts.hound_ism_bed) (in module baskerville.scripts.hound_ism_snp) (in module baskerville.scripts.hound_predbed) (in module baskerville.scripts.hound_snp) (in module baskerville.scripts.hound_snpgene) (in module baskerville.scripts.hound_train) make_alt_1hot() (in module baskerville.snps) make_bed_seqs() (in module baskerville.bed) make_dataset() (baskerville.dataset.SeqDataset method) make_gene_bedt() (in module baskerville.snps) make_net_graph() (in module baskerville.scripts.hound_data_align) make_optimizer() (baskerville.trainer.Trainer method) make_snp_bedt() (in module baskerville.snps) make_strand_transform() (in module baskerville.dataset) map_snps_genes() (in module baskerville.snps) mean_squared_error_udot() (in module baskerville.metrics) MeanSquaredErrorUDot (class in baskerville.metrics) midpoint() (baskerville.gene.Gene method) ModelOptimizer (class in baskerville.helpers.tensorrt_helpers) ModelSeq (class in baskerville.data) module baskerville baskerville.bed baskerville.blocks baskerville.data baskerville.dataset baskerville.dna baskerville.gene baskerville.helpers baskerville.helpers.gcs_utils baskerville.helpers.h5_baskerville_utils baskerville.helpers.h5_utils baskerville.helpers.tensorrt_helpers baskerville.helpers.trt_optimized_model baskerville.helpers.utils baskerville.layers baskerville.metrics baskerville.scripts baskerville.scripts.hound_data baskerville.scripts.hound_data_align baskerville.scripts.hound_data_read baskerville.scripts.hound_data_write baskerville.scripts.hound_eval baskerville.scripts.hound_eval_spec baskerville.scripts.hound_ism_bed baskerville.scripts.hound_ism_snp baskerville.scripts.hound_predbed baskerville.scripts.hound_snp baskerville.scripts.hound_snpgene baskerville.scripts.hound_train baskerville.seqnn baskerville.snps baskerville.trainer baskerville.vcf

MultiheadAttention (class in baskerville.layers)

N

net (baskerville.scripts.hound_data_align.GraphSeq attribute)

num_targets() (baskerville.seqnn.SeqNN method) numpy() (baskerville.dataset.SeqDataset method)

O

on_epoch_end() (baskerville.trainer.EarlyStoppingMin method) one_to_two() (in module baskerville.blocks)

OneToTwo (class in baskerville.layers) OptimizedModel (class in baskerville.helpers.trt_optimized_model) output_slice() (baskerville.gene.Gene method)

P

parse_loss() (in module baskerville.trainer) PearsonR (class in baskerville.metrics) poisson() (in module baskerville.metrics) poisson_kl() (in module baskerville.metrics) poisson_multinomial() (in module baskerville.metrics) PoissonKL (class in baskerville.metrics)

PoissonMultinomial (class in baskerville.metrics) positional_features() (in module baskerville.layers) positional_features_central_mask() (in module baskerville.layers) predict() (baskerville.helpers.trt_optimized_model.OptimizedModel method) (baskerville.seqnn.SeqNN method) predict_transform() (baskerville.seqnn.SeqNN method) preprocess_bed() (baskerville.scripts.hound_data_read.CovFace method)

Q

quantify_leakage() (in module baskerville.scripts.hound_data_align)

R

R2 (class in baskerville.metrics) read() (baskerville.scripts.hound_data_read.CovFace method) read_bed_coords() (in module baskerville.bed) read_blacklist() (in module baskerville.scripts.hound_data_read) read_gtf() (baskerville.gene.Transcriptome method) rejoin_large_contigs() (in module baskerville.data) relative_shift() (in module baskerville.layers) report_divide_stats() (in module baskerville.scripts.hound_data_align)

report_divide_stats_v1() (in module baskerville.scripts.hound_data_align) res_tower() (in module baskerville.blocks) reset_state() (baskerville.metrics.PearsonR method) (baskerville.metrics.R2 method) restore() (baskerville.seqnn.SeqNN method) result() (baskerville.metrics.PearsonR method) (baskerville.metrics.R2 method) (baskerville.metrics.SeqAUC method) rround() (in module baskerville.scripts.hound_data_write)

S

safe_next() (in module baskerville.trainer) save() (baskerville.helpers.tensorrt_helpers.ModelOptimizer method) (baskerville.seqnn.SeqNN method) Scale (class in baskerville.layers) score_gene_snps() (in module baskerville.snps) score_snps() (in module baskerville.snps) SeqAUC (class in baskerville.metrics) SeqDataset (class in baskerville.dataset) SeqNN (class in baskerville.seqnn) set_calibration_data() (baskerville.helpers.tensorrt_helpers.ModelOptimizer method) set_defaults() (baskerville.seqnn.SeqNN method) shift_sequence() (in module baskerville.layers) SNP (class in baskerville.vcf) snp_seq1() (in module baskerville.vcf) SNPCluster (class in baskerville.snps) snps2_seq1() (in module baskerville.vcf) snps_seq1() (in module baskerville.vcf) SoftmaxPool1D (class in baskerville.layers)

Softplus (class in baskerville.layers) span() (baskerville.gene.Gene method) split_contigs() (in module baskerville.data) split_gcs_uri() (in module baskerville.helpers.gcs_utils) squeeze_excite() (in module baskerville.blocks) SqueezeExcite (class in baskerville.layers) start (baskerville.data.Contig attribute) (baskerville.data.ModelSeq attribute) (baskerville.scripts.hound_data_align.GraphSeq attribute) step() (baskerville.seqnn.SeqNN method) stitch_preds() (in module baskerville.snps) StochasticReverseComplement (class in baskerville.layers) StochasticShift (class in baskerville.layers) swin_transformer() (in module baskerville.blocks) SwitchReverse (class in baskerville.layers) SwitchReverseTriu (class in baskerville.layers) Symmetrize2D (class in baskerville.layers) symmetrize_2d() (in module baskerville.blocks) sync_dir_to_gcs() (in module baskerville.helpers.gcs_utils)

T

targets_prep_strand() (in module baskerville.dataset) tconv_nac() (in module baskerville.blocks) track_sequence() (baskerville.seqnn.SeqNN method) Trainer (class in baskerville.trainer) Transcriptome (class in baskerville.gene)

transformer() (in module baskerville.blocks) transformer2() (in module baskerville.blocks) transformer_dense() (in module baskerville.blocks) transformer_split() (in module baskerville.blocks) transformer_tower() (in module baskerville.blocks) tround() (in module baskerville.scripts.hound_data_write)

U

unet_concat() (in module baskerville.blocks) unet_conv() (in module baskerville.blocks) unitwise_norm() (in module baskerville.trainer) untransform_preds() (in module baskerville.dataset) untransform_preds1() (in module baskerville.dataset) update_state() (baskerville.metrics.PearsonR method) (baskerville.metrics.R2 method) (baskerville.metrics.SeqAUC method)

upload_file_gcs() (in module baskerville.helpers.gcs_utils) upload_folder_gcs() (in module baskerville.helpers.gcs_utils) upper_tri() (in module baskerville.blocks) UpperTri (class in baskerville.layers)

V

vcf_count() (in module baskerville.vcf) vcf_line (baskerville.vcf.SNP attribute)

vcf_snps() (in module baskerville.vcf) vcf_sort() (in module baskerville.vcf)

W

WarmUp (class in baskerville.trainer) wheeze_excite() (in module baskerville.blocks) WheezeExcite (class in baskerville.layers) write_bed_exon() (baskerville.gene.Transcriptome method)

write_bed_span() (baskerville.gene.Transcriptome method) write_bedgraph() (in module baskerville.bed) write_pct() (in module baskerville.snps) write_seqs_bed() (in module baskerville.data) write_snp() (in module baskerville.snps)