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Contents

ALLCools.reptile.reptile

Module Contents

_create_train_region_ds(reptile)

_create_train_dmr_ds(reptile, train_regions_bed, train_label)

_create_query_region_ds(reptile)

_create_query_dmr_ds(reptile, dmr_regions_bed_df)

_get_data_and_label(region_ds, modalities, sample, fillna_by_zero_list)

_predict_sample(region_ds_path, region_dim, modalities, fillna_by_zero, sample, output_path, mask_cutoff=0.3, chunk_size=100000)

_call_enhancer_region(bw_path, dmr_bed, threshold, merge_dist, chrom_size_path)

class REPTILE(output_path, train_regions, dmr_regions, train_region_labels, train_sample, bigwig_table, chrom_size_path, window_size=2000, step_size=200, dmr_slop=150, fillna_by_zero=None)

generate_region_ds(self)

property train_region_ds(self)

property train_dmr_ds(self)

property query_region_ds(self)

property query_dmr_ds(self)

property region_model(self)

property dmr_model(self)

_validate_region_name(self, name)

annotate_by_bigwigs(self, name, slop, cpu, redo=False)

_filter_na_train(self, name, sample, max_na_rate=0.5)

prepare_training_input(self, name)

static auto_ml(data, label, output_path, train_size=0.75, random_state=42, cpu=1, tpot_generations=5, tpot_max_time_mins=60, **tpot_kwargs)

_train(self, region_dim, slop, cpu, **kwargs)

train_region_model(self, slop=None, cpu=1, **kwargs)

train_dmr_model(self, slop=None, cpu=1, **kwargs)

fit(self, cpu=10, **kwargs)

Convenient function to train everything by default parameters

_predict(self, region_dim, cpu, mask_cutoff)

predict(self, cpu, mask_cutoff=0.3, bw_bin_size=10, enhancer_cutoff=0.7)

_dump_sample(self, sample, mask_cutoff, bw_bin_size)

dump_bigwigs(self, cpu, mask_cutoff, bw_bin_size)

call_enhancers(self, threshold=0.7, merge_dist=None)

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