DNADNA
Contents:
Introduction
Usage Overview
Tutorials
Configuration Format
Simulation Datasets
Dataset Preprocessing
Model Training
Prediction
Using and Implementing Simulators
Configuration Schemas
Extending DNADNA with Plugins
Development
API Documentation
DNADNA
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Index
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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Y
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Z
A
AverageMeter (class in dnadna.utils.misc)
B
BaseYAMLDumper (class in dnadna.utils.yaml)
binary (dnadna.utils.serializers.GenericSerializer attribute)
BUILTIN_PLUGINS (in module dnadna)
C
cache() (dnadna.utils.decorators.cached_classproperty method)
(dnadna.utils.decorators.cached_property method)
cached_classproperty (class in dnadna.utils.decorators)
cached_property (class in dnadna.utils.decorators)
cached_set (dnadna.datasets.DNADataset property)
capture_stdio (class in dnadna.utils.misc)
check_scenario() (dnadna.data_preprocessing.DataPreprocessor method)
check_scenarios() (dnadna.data_preprocessing.DataPreprocessor method)
check_snp_sample() (dnadna.data_preprocessing.DataPreprocessor static method)
class_from_config() (dnadna.simulator.Simulator class method)
classproperty (class in dnadna.utils.decorators)
CNN (class in dnadna.nets)
collate_batch() (dnadna.datasets.DatasetTransformationMixIn static method)
Command (class in dnadna.utils.cli)
CommandWithPlugins (class in dnadna.utils.cli)
CommentedEmitter (class in dnadna.utils.yaml)
CommentedMapping (class in dnadna.utils.yaml)
CommentedMappingNode (class in dnadna.utils.yaml)
CommentedNode (class in dnadna.utils.yaml)
CommentedRepresenter (class in dnadna.utils.yaml)
CommentedScalarNode (class in dnadna.utils.yaml)
CommentedSerializer (class in dnadna.utils.yaml)
CommentedYAMLDumper (class in dnadna.utils.yaml)
CommentEvent (class in dnadna.utils.yaml)
Compose (class in dnadna.transforms)
concat (dnadna.snp_sample.SNPSample property)
Config (class in dnadna.utils.config)
config (dnadna.params.LearnedParams attribute)
config_attr (dnadna.utils.config.ConfigMixIn attribute)
config_default (dnadna.simulator.Simulator attribute)
(dnadna.utils.config.ConfigMixIn attribute)
config_filename_format (dnadna.simulator.Simulator attribute)
config_schema (dnadna.simulator.Simulator attribute)
(dnadna.utils.config.ConfigMixIn attribute)
ConfigError
ConfigMixIn (class in dnadna.utils.config)
configure_logging() (dnadna.utils.cli.Command class method)
ConfigValidator (class in dnadna.utils.config)
ConfigValidatorMixin (class in dnadna.utils.jsonschema)
consume() (in module dnadna.utils.misc)
convert_from() (dnadna.snp_sample.DictSNPConverter class method)
(dnadna.snp_sample.NpzSNPConverter class method)
(dnadna.snp_sample.SNPConverter class method)
convert_to() (dnadna.snp_sample.DictSNPConverter method)
(dnadna.snp_sample.NpzSNPConverter method)
(dnadna.snp_sample.SNPConverter method)
converter_formats (dnadna.snp_sample.SNPSample property)
converters (dnadna.snp_sample.SNPConverter property)
copy() (dnadna.snp_sample.SNPSample method)
(dnadna.utils.config.Config method)
(dnadna.utils.config.DeepChainMap method)
copy_with() (dnadna.snp_sample.SNPSample method)
create_argument_parser() (dnadna.utils.cli.Command class method)
(dnadna.utils.cli.CommandWithPlugins class method)
Crop (class in dnadna.transforms)
CustomCNN (class in dnadna.nets)
CustomValidationError
cut_and_cat() (in module dnadna.utils.tensor)
D
DataPreprocessor (class in dnadna.data_preprocessing)
dataset (dnadna.training.ModelTrainer property)
DatasetTransformationMixIn (class in dnadna.datasets)
decamelcase() (in module dnadna.utils.misc)
DeepChainMap (class in dnadna.utils.config)
DEFAULT_NPZ_FILENAME_FORMAT (dnadna.datasets.NpzSNPSource attribute)
default_plugins (dnadna.utils.cli.CommandWithPlugins attribute)
DEFAULTS_DIR (in module dnadna)
desphinxify() (in module dnadna.utils.misc)
DESPHINXIFY_REF_ROLES (in module dnadna.utils.misc)
device (dnadna.training.ModelTrainer property)
dict() (dnadna.utils.config.DeepChainMap method)
dict_merge() (in module dnadna.utils.misc)
dict_slice() (in module dnadna.utils.misc)
DictSerializer (class in dnadna.utils.serializers)
DictSNPConverter (class in dnadna.snp_sample)
DictSNPSource (class in dnadna.datasets)
DNADataset (class in dnadna.datasets)
dnadna
module
dnadna.data_preprocessing
module
dnadna.datasets
module
dnadna.examples
module
dnadna.examples.one_event
module
dnadna.nets
module
dnadna.params
module
dnadna.simulation
module
dnadna.simulator
module
dnadna.snp_sample
module
dnadna.training
module
dnadna.transforms
module
dnadna.utils
module
dnadna.utils.cli
module
dnadna.utils.config
module
dnadna.utils.decorators
module
dnadna.utils.jsonschema
module
dnadna.utils.misc
module
dnadna.utils.plugins
module
dnadna.utils.serializers
module
dnadna.utils.tensor
module
dnadna.utils.yaml
module
DNADNAFilter (class in dnadna.utils.cli)
DNADNANet (in module dnadna.nets)
DNADNAWarning
DNATrainingDataset (class in dnadna.datasets)
DummySummaryWriter (class in dnadna.training)
E
ensure_run_dir() (dnadna.training.ModelTrainer method)
error_log (dnadna.training.ModelTrainer property)
F
FileListSNPSource (class in dnadna.datasets)
filename_or_obj() (in module dnadna.utils.serializers)
filter() (dnadna.utils.cli.DNADNAFilter method)
first_paragraph() (in module dnadna.utils.misc)
flatten() (in module dnadna.utils.misc)
format (dnadna.snp_sample.SNPConverter property)
format_docstring() (in module dnadna.utils.decorators)
(in module dnadna.utils.misc)
format_to_re() (in module dnadna.utils.misc)
formats (dnadna.snp_sample.SNPConverter property)
forward (dnadna.nets.Network property)
forward() (dnadna.nets.CNN method)
(dnadna.nets.CustomCNN method)
(dnadna.nets.MLP method)
(dnadna.nets.SPIDNA method)
(dnadna.nets.SPIDNABlock method)
(dnadna.params.MCELoss method)
from_config() (dnadna.datasets.NpzSNPSource class method)
(dnadna.datasets.SNPSource class method)
from_config_file() (dnadna.datasets.DNADataset class method)
(dnadna.datasets.DNATrainingDataset class method)
(dnadna.datasets.SNPSource class method)
(dnadna.training.ModelTrainer class method)
(dnadna.utils.config.ConfigMixIn class method)
from_default() (dnadna.utils.config.Config class method)
from_dict() (dnadna.snp_sample.DictSNPConverter class method)
from_file() (dnadna.snp_sample.SNPSample class method)
(dnadna.utils.config.Config class method)
from_npz() (dnadna.snp_sample.NpzSNPConverter class method)
full_net_params (dnadna.training.ModelTrainer property)
full_pos_format (dnadna.snp_sample.SNPSample property)
G
gen_name_params_schema() (in module dnadna.utils.plugins)
generate_scenario_params() (dnadna.examples.one_event.OneEventSimulator method)
(dnadna.simulator.Simulator method)
generation_time (dnadna.examples.one_event.OneEventSimulator attribute)
GenericSerializer (class in dnadna.utils.serializers)
get() (dnadna.datasets.DatasetTransformationMixIn method)
(dnadna.datasets.DNADataset method)
get_data() (dnadna.snp_sample.DictSNPConverter method)
(dnadna.snp_sample.NpzSNPConverter method)
(dnadna.snp_sample.SNPLoader method)
get_owner() (dnadna.utils.config.DeepChainMap method)
get_plugin() (dnadna.utils.plugins.Pluggable class method)
get_plugins() (dnadna.utils.plugins.Pluggable class method)
get_resolver_for() (dnadna.utils.jsonschema.ConfigValidatorMixin class method)
get_run_info() (dnadna.training.ModelTrainer method)
get_schema() (dnadna.nets.Network class method)
(dnadna.simulator.Simulator class method)
(dnadna.transforms.Transform class method)
(dnadna.utils.plugins.Pluggable class method)
get_shape() (dnadna.snp_sample.NpzSNPConverter method)
(dnadna.snp_sample.SNPLoader method)
H
hidden (dnadna.utils.cli.Command attribute)
I
indent() (in module dnadna.utils.misc)
init_data_loaders() (dnadna.training.ModelTrainer method)
invalidate() (dnadna.utils.decorators.cached_property method)
InvalidSNPSample
items() (dnadna.utils.config.DeepChainMap method)
J
JSONSerializer (class in dnadna.utils.serializers)
K
keep_polymorphic_only() (in module dnadna.transforms)
keys() (dnadna.utils.config.DeepChainMap method)
L
language (dnadna.utils.serializers.DictSerializer attribute)
(dnadna.utils.serializers.GenericSerializer attribute)
learned_params (dnadna.training.ModelTrainer property)
LearnedParams (class in dnadna.params)
load() (dnadna.snp_sample.NpzSNPConverter class method)
(dnadna.utils.serializers.GenericSerializer class method)
(dnadna.utils.serializers.JSONSerializer class method)
(dnadna.utils.serializers.YAMLSerializer class method)
load_dict() (in module dnadna.utils.config)
load_dict_from_json() (in module dnadna.utils.config)
load_plugins() (in module dnadna.utils.plugins)
load_scenario_params() (dnadna.simulator.Simulator method)
loaded_plugins() (in module dnadna.utils.plugins)
loader (dnadna.snp_sample.SNPSample property)
logging_args (dnadna.utils.cli.Command attribute)
logging_config (dnadna.utils.cli.Command attribute)
loss_funcs (dnadna.params.LearnedParams property)
(dnadna.training.ModelTrainer property)
loss_weights (dnadna.params.LearnedParams property)
(dnadna.training.ModelTrainer property)
lru_cache_with_dict() (in module dnadna.utils.decorators)
M
make_config_meta_schema() (in module dnadna.utils.jsonschema)
make_config_validator() (in module dnadna.utils.jsonschema)
maps (dnadna.utils.config.DeepChainMap attribute)
match_filename() (dnadna.utils.serializers.GenericSerializer class method)
MCELoss (class in dnadna.params)
MissingSNPSample
MLP (class in dnadna.nets)
ModelTrainer (class in dnadna.training)
module
dnadna
dnadna.data_preprocessing
dnadna.datasets
dnadna.examples
dnadna.examples.one_event
dnadna.nets
dnadna.params
dnadna.simulation
dnadna.simulator
dnadna.snp_sample
dnadna.training
dnadna.transforms
dnadna.utils
dnadna.utils.cli
dnadna.utils.config
dnadna.utils.decorators
dnadna.utils.jsonschema
dnadna.utils.misc
dnadna.utils.plugins
dnadna.utils.serializers
dnadna.utils.tensor
dnadna.utils.yaml
multi_representer() (in module dnadna.utils.yaml)
mutation_rate (dnadna.examples.one_event.OneEventSimulator attribute)
N
n_indiv (dnadna.snp_sample.SNPSample property)
n_max (dnadna.examples.one_event.OneEventSimulator attribute)
n_min (dnadna.examples.one_event.OneEventSimulator attribute)
n_outputs (dnadna.params.ParamSet property)
(dnadna.training.ModelTrainer property)
n_replicates (dnadna.examples.one_event.OneEventSimulator attribute)
n_samples (dnadna.examples.one_event.OneEventSimulator attribute)
n_scenarios (dnadna.examples.one_event.OneEventSimulator attribute)
n_snp (dnadna.snp_sample.SNPSample property)
name (dnadna.simulator.Simulator property)
(dnadna.utils.plugins.Pluggable attribute)
nanmean() (in module dnadna.utils.tensor)
net (dnadna.training.ModelTrainer property)
Network (class in dnadna.nets)
normpath() (in module dnadna.utils.jsonschema)
NpzSNPConverter (class in dnadna.snp_sample)
NpzSNPSource (class in dnadna.datasets)
O
ONE_EVENT_CONFIG_SCHEMA (in module dnadna.examples.one_event)
OneEventSimulator (class in dnadna.examples.one_event)
optimizer (dnadna.training.ModelTrainer property)
overrides (dnadna.utils.config.DeepChainMap attribute)
P
param_names (dnadna.params.ParamSet property)
(dnadna.training.ModelTrainer property)
param_slices (dnadna.params.ParamSet property)
params (dnadna.params.ParamSet property)
ParamSet (class in dnadna.params)
parse_format() (in module dnadna.utils.misc)
path (dnadna.snp_sample.SNPSample property)
Pluggable (class in dnadna.utils.plugins)
plugin_registered() (dnadna.utils.plugins.Pluggable class method)
plugin_url (dnadna.utils.plugins.Pluggable attribute)
pos (dnadna.snp_sample.SNPSample property)
pos_format (dnadna.snp_sample.SNPSample property)
prepare() (dnadna.training.ModelTrainer method)
prepared_property (class in dnadna.training)
preparse_args() (dnadna.utils.cli.Command static method)
(dnadna.utils.cli.CommandWithPlugins class method)
preprocess_scenario_params() (dnadna.data_preprocessing.DataPreprocessor method)
preprocessing_config_default (dnadna.simulator.Simulator attribute)
product (dnadna.snp_sample.SNPSample property)
R
recombination_rate (dnadna.examples.one_event.OneEventSimulator attribute)
reformat_format() (in module dnadna.utils.misc)
ReformatPosition (class in dnadna.transforms)
relevance_with_const_select() (dnadna.utils.jsonschema.ConfigValidatorMixin static method)
representer() (in module dnadna.utils.yaml)
retrieve() (dnadna.utils.decorators.cached_property method)
Rotate (class in dnadna.transforms)
run() (dnadna.utils.cli.Command class method)
run_dir (dnadna.training.ModelTrainer property)
run_id (dnadna.training.ModelTrainer property)
run_name (dnadna.training.ModelTrainer property)
run_training() (dnadna.training.ModelTrainer method)
S
save() (dnadna.snp_sample.NpzSNPConverter class method)
(dnadna.utils.serializers.GenericSerializer class method)
(dnadna.utils.serializers.JSONSerializer class method)
(dnadna.utils.serializers.YAMLSerializer class method)
save_checkpoints (dnadna.training.ModelTrainer property)
save_dict() (in module dnadna.utils.config)
save_dict_annotated() (in module dnadna.utils.config)
save_dict_in_json() (in module dnadna.utils.config)
save_net() (dnadna.training.ModelTrainer method)
scenario_params (dnadna.params.LearnedParams property)
ScenarioValidationError
schema (dnadna.nets.Network attribute)
(dnadna.utils.plugins.Pluggable attribute)
SCHEMA_DIRS (in module dnadna.utils.jsonschema)
schemas (dnadna.utils.config.Config property)
segment_length (dnadna.examples.one_event.OneEventSimulator attribute)
sentinel (dnadna.utils.decorators.cached_property attribute)
serializer_for() (dnadna.utils.serializers.GenericSerializer class method)
shape (dnadna.snp_sample.SNPSample property)
simulate_scenario() (dnadna.examples.one_event.OneEventSimulator method)
(dnadna.simulator.Simulator method)
simulate_scenarios() (dnadna.simulator.Simulator method)
Simulation (class in dnadna.simulation)
Simulator (class in dnadna.simulator)
snp (dnadna.snp_sample.SNPSample property)
SNPConverter (class in dnadna.snp_sample)
SnpFormat (class in dnadna.transforms)
SNPLoader (class in dnadna.snp_sample)
SNPSample (class in dnadna.snp_sample)
SNPSerializer (class in dnadna.snp_sample)
SNPSource (class in dnadna.datasets)
SPIDNA (class in dnadna.nets)
SPIDNABlock (class in dnadna.nets)
stdio_redirect_tqdm (class in dnadna.utils.misc)
store() (dnadna.utils.decorators.cached_property method)
str_or_int() (in module dnadna.utils.cli)
Subsample (class in dnadna.transforms)
T
tensor (dnadna.snp_sample.SNPSample property)
tensor_format (dnadna.snp_sample.SNPSample property)
test_set (dnadna.datasets.DatasetTransformationMixIn property)
timestamp() (in module dnadna.utils.jsonschema)
tmax (dnadna.examples.one_event.OneEventSimulator attribute)
tmin (dnadna.examples.one_event.OneEventSimulator attribute)
to() (dnadna.params.LearnedParams method)
to_dict() (dnadna.snp_sample.DictSNPConverter method)
to_file() (dnadna.snp_sample.SNPSample method)
(dnadna.utils.config.Config method)
to_filename() (dnadna.utils.serializers.GenericSerializer static method)
to_npz() (dnadna.snp_sample.NpzSNPConverter method)
to_tensor() (in module dnadna.utils.tensor)
training_config_default (dnadna.simulator.Simulator attribute)
training_loader (dnadna.training.ModelTrainer property)
training_set (dnadna.datasets.DatasetTransformationMixIn property)
Transform (class in dnadna.transforms)
TransformException
transforms (dnadna.datasets.DatasetTransformationMixIn property)
types (dnadna.utils.serializers.DictSerializer attribute)
(dnadna.utils.serializers.GenericSerializer property)
U
unique() (in module dnadna.utils.misc)
unresolve_inherits() (dnadna.utils.config.Config method)
V
validate() (dnadna.utils.config.Config method)
(dnadna.utils.config.ConfigValidator method)
(dnadna.utils.jsonschema.ConfigValidatorMixin method)
validate_config() (dnadna.data_preprocessing.DataPreprocessor method)
(dnadna.utils.config.ConfigMixIn method)
ValidateSnp (class in dnadna.transforms)
validation_loader (dnadna.training.ModelTrainer property)
validation_set (dnadna.datasets.DatasetTransformationMixIn property)
values() (dnadna.utils.config.DeepChainMap method)
Y
YAMLDumper (class in dnadna.utils.yaml)
YAMLSerializer (class in dnadna.utils.serializers)
Z
zero_pad_format() (in module dnadna.utils.misc)