baskerville documentation

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Contents:

• baskerville package
  • Subpackages
    • baskerville.helpers package
      • Submodules
      • 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
      • Module contents
    • baskerville.scripts package
      • Submodules
      • 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_snp_slurm module
      • baskerville.scripts.hound_snpgene module
      • baskerville.scripts.hound_train module
      • Module contents
  • Submodules
  • baskerville.bed module
    • make_bed_seqs()
    • read_bed_coords()
    • write_bedgraph()
  • baskerville.blocks module
    • center_average()
    • center_slice()
    • concat_dist_2d()
    • concat_position()
    • conv_block()
    • conv_block_2d()
    • conv_dna()
    • conv_nac()
    • conv_next()
    • conv_tower()
    • conv_tower_nac()
    • conv_tower_v1()
    • convnext_tower()
    • cropping_2d()
    • dense_block()
    • dense_nac()
    • dilated_dense()
    • dilated_residual()
    • dilated_residual_2d()
    • dilated_residual_nac()
    • factor_inverse()
    • final()
    • global_context()
    • one_to_two()
    • res_tower()
    • squeeze_excite()
    • swin_transformer()
    • symmetrize_2d()
    • tconv_nac()
    • transformer()
    • transformer2()
    • transformer_dense()
    • transformer_split()
    • transformer_tower()
    • unet_concat()
    • unet_conv()
    • upper_tri()
    • wheeze_excite()
  • baskerville.data module
    • Contig
      • Contig.chr
      • Contig.end
      • Contig.genome
      • Contig.start
    • ModelSeq
      • ModelSeq.chr
      • ModelSeq.end
      • ModelSeq.genome
      • ModelSeq.label
      • ModelSeq.start
    • annotate_unmap()
    • break_large_contigs()
    • contig_sequences()
    • load_chromosomes()
    • rejoin_large_contigs()
    • split_contigs()
    • write_seqs_bed()
  • baskerville.dataset module
    • SeqDataset
      • SeqDataset.batches_per_epoch()
      • SeqDataset.compute_stats()
      • SeqDataset.distribute()
      • SeqDataset.generate_parser()
      • SeqDataset.make_dataset()
      • SeqDataset.numpy()
    • file_to_records()
    • make_strand_transform()
    • targets_prep_strand()
    • untransform_preds()
    • untransform_preds1()
  • baskerville.dna module
    • dna_1hot()
    • dna_1hot_index()
    • dna_rc()
    • hot1_augment()
    • hot1_delete()
    • hot1_dna()
    • hot1_get()
    • hot1_insert()
    • hot1_rc()
    • hot1_set()
  • baskerville.gene module
    • Gene
      • Gene.add_exon()
      • Gene.get_exons()
      • Gene.midpoint()
      • Gene.output_slice()
      • Gene.span()
    • GenomicInterval
    • Transcriptome
      • Transcriptome.bedtool_exon()
      • Transcriptome.bedtool_span()
      • Transcriptome.read_gtf()
      • Transcriptome.write_bed_exon()
      • Transcriptome.write_bed_span()
    • gtf_kv()
  • baskerville.layers module
    • CenterAverage
      • CenterAverage.call()
      • CenterAverage.get_config()
    • CenterSlice
      • CenterSlice.call()
      • CenterSlice.get_config()
    • ConcatDist2D
      • ConcatDist2D.call()
    • ConcatPosition
      • ConcatPosition.call()
      • ConcatPosition.get_config()
    • EnsembleReverseComplement
      • EnsembleReverseComplement.call()
    • EnsembleShift
      • EnsembleShift.call()
      • EnsembleShift.get_config()
    • FactorInverse
      • FactorInverse.call()
      • FactorInverse.get_config()
    • GlobalContext
      • GlobalContext.build()
      • GlobalContext.call()
    • LengthAverage
      • LengthAverage.call()
    • MultiheadAttention
      • MultiheadAttention.call()
      • MultiheadAttention.get_config()
    • OneToTwo
      • OneToTwo.call()
      • OneToTwo.get_config()
    • Scale
      • Scale.build()
      • Scale.call()
      • Scale.get_config()
    • SoftmaxPool1D
      • SoftmaxPool1D.build()
      • SoftmaxPool1D.call()
      • SoftmaxPool1D.get_config()
    • Softplus
      • Softplus.call()
      • Softplus.get_config()
    • SqueezeExcite
      • SqueezeExcite.build()
      • SqueezeExcite.call()
      • SqueezeExcite.get_config()
    • StochasticReverseComplement
      • StochasticReverseComplement.call()
    • StochasticShift
      • StochasticShift.call()
      • StochasticShift.get_config()
    • SwitchReverse
      • SwitchReverse.call()
      • SwitchReverse.get_config()
    • SwitchReverseTriu
      • SwitchReverseTriu.call()
      • SwitchReverseTriu.get_config()
    • Symmetrize2D
      • Symmetrize2D.call()
    • UpperTri
      • UpperTri.call()
      • UpperTri.get_config()
    • WheezeExcite
      • WheezeExcite.build()
      • WheezeExcite.call()
      • WheezeExcite.get_config()
    • activate()
    • positional_features()
    • positional_features_central_mask()
    • relative_shift()
    • shift_sequence()
  • baskerville.metrics module
    • MeanSquaredErrorUDot
    • PearsonR
      • PearsonR.reset_state()
      • PearsonR.result()
      • PearsonR.update_state()
    • PoissonKL
    • PoissonMultinomial
    • R2
      • R2.reset_state()
      • R2.result()
      • R2.update_state()
    • SeqAUC
      • SeqAUC.interpolate_pr_auc()
      • SeqAUC.result()
      • SeqAUC.update_state()
    • mean_squared_error_udot()
    • poisson()
    • poisson_kl()
    • poisson_multinomial()
  • baskerville.seqnn module
    • SeqNN
      • SeqNN.build_block()
      • SeqNN.build_embed()
      • SeqNN.build_ensemble()
      • SeqNN.build_model()
      • SeqNN.build_sad()
      • SeqNN.build_slice()
      • SeqNN.downcast()
      • SeqNN.evaluate()
      • SeqNN.get_bn_layer()
      • SeqNN.get_conv_layer()
      • SeqNN.get_conv_weights()
      • SeqNN.get_dense_layer()
      • SeqNN.gradients()
      • SeqNN.gradients_func()
      • SeqNN.gradients_func_orig()
      • SeqNN.gradients_orig()
      • SeqNN.num_targets()
      • SeqNN.predict()
      • SeqNN.predict_transform()
      • SeqNN.restore()
      • SeqNN.save()
      • SeqNN.set_defaults()
      • SeqNN.step()
      • SeqNN.track_sequence()
  • baskerville.snps module
    • GeneSNPCluster
      • GeneSNPCluster.add_gene()
      • GeneSNPCluster.delimit()
    • SNPCluster
      • SNPCluster.add_snp()
      • SNPCluster.delimit()
      • SNPCluster.get_1hots()
    • cluster_genes()
    • cluster_snps()
    • compute_scores()
    • initialize_output_h5()
    • make_alt_1hot()
    • make_gene_bedt()
    • make_snp_bedt()
    • map_snps_genes()
    • score_gene_snps()
    • score_snps()
    • stitch_preds()
    • write_pct()
    • write_snp()
  • baskerville.trainer module
    • Cyclical1LearningRate
      • Cyclical1LearningRate.get_config()
    • EarlyStoppingMin
      • EarlyStoppingMin.on_epoch_end()
    • Trainer
      • Trainer.compile()
      • Trainer.fit2()
      • Trainer.fit_keras()
      • Trainer.fit_tape()
      • Trainer.make_optimizer()
    • WarmUp
      • WarmUp.get_config()
    • adaptive_clip_grad()
    • compute_norm()
    • parse_loss()
    • safe_next()
    • unitwise_norm()
  • baskerville.vcf module
    • SNP
      • SNP.vcf_line
      • SNP.flip_alleles()
      • SNP.get_alleles()
      • SNP.indel_size()
      • SNP.longest_alt()
    • cap_allele()
    • dna_length_1hot()
    • intersect_seqs_snps()
    • intersect_snps_seqs()
    • snp_seq1()
    • snps2_seq1()
    • snps_seq1()
    • vcf_count()
    • vcf_snps()
    • vcf_sort()
  • Module contents