omnigenome 0.3.0a0__py3-none-any.whl

omnigenome/__init__.py

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+# -*- coding: utf-8 -*-
+# file: __init__.py
+# time: 14:53 06/04/2024
+# author: YANG, HENG <hy345@exeter.ac.uk> (杨恒)
+# github: https://github.com/yangheng95
+# huggingface: https://huggingface.co/yangheng
+# google scholar: https://scholar.google.com/citations?user=NPq5a_0AAAAJ&hl=en
+# Copyright (C) 2019-2024. All Rights Reserved.
+
+"""
+OmniGenome: A comprehensive toolkit for genomic foundation models.
+
+This package provides a suite of tools for working with genomic data, including:
+- Automated benchmarking and training pipelines.
+- A hub for accessing pre-trained models, datasets, and pipelines.
+- A flexible and extensible framework for building custom models and tasks.
+
+This __init__.py file exposes the core components of the library for easy access.
+
+Key Components:
+---------------
+- AutoBench: Automated benchmarking of genomic models
+- AutoTrain: Automated training of genomic models  
+- BenchHub: Hub for accessing benchmarks
+- ModelHub: Hub for accessing pre-trained models
+- PipelineHub: Hub for accessing pipelines
+- Various model classes for different genomic tasks
+- Dataset classes for different data formats
+- Tokenizer classes for different sequence representations
+- Metric classes for evaluation
+- Trainer classes for model training
+
+Example Usage:
+--------------
+```python
+from omnigenome import AutoBench, AutoTrain, OmniModelForSequenceClassification
+
+# Run automated benchmarking
+bench = AutoBench("RGB", "model_name")
+bench.run()
+
+# Train a model
+trainer = AutoTrain("RGB", "model_name")
+trainer.run()
+
+# Use a specific model
+model = OmniModelForSequenceClassification("model_path", tokenizer)
+```
+"""
+
+__name__ = "omnigenome"
+__version__ = "0.3.0alpha"
+
+__author__ = "YANG, HENG"
+__email__ = "yangheng2021@gmail.com"
+__license__ = "Apache-2.0"
+
+# Import core auto components
+from .auto.auto_bench.auto_bench import AutoBench
+from .auto.auto_bench.auto_bench_config import AutoBenchConfig
+from .auto.bench_hub.bench_hub import BenchHub
+from .auto.auto_train.auto_train import AutoTrain
+from .auto.auto_bench.auto_bench_cli import run_bench, bench_command
+from .auto.auto_train.auto_train_cli import run_train, train_command
+
+# Import source modules
+from .src import dataset as dataset
+from .src import metric as metric
+from .src import model as model
+from .src import tokenizer as tokenizer
+
+# Import abstract base classes
+from .src.abc.abstract_dataset import OmniDataset
+from .src.abc.abstract_metric import OmniMetric
+from .src.abc.abstract_model import OmniModel
+from .src.abc.abstract_tokenizer import OmniTokenizer
+from .src.abc.abstract_tokenizer import OmniTokenizer as AutoTokenizer
+
+# Import dataset classes
+from .src.dataset.omni_dataset import OmniDatasetForSequenceClassification
+from .src.dataset.omni_dataset import OmniDatasetForSequenceRegression
+from .src.dataset.omni_dataset import OmniDatasetForTokenClassification
+from .src.dataset.omni_dataset import OmniDatasetForTokenRegression
+
+# Import metric classes
+from .src.metric import ClassificationMetric, RegressionMetric, RankingMetric
+
+# Import utility functions
+from .src.misc import utils as utils
+from .src.misc.utils import clean_temp_dir_pt_files
+
+# Import model classes
+from .src.model import (
+    OmniModelForSequenceClassification,
+    OmniModelForMultiLabelSequenceClassification,
+    OmniModelForTokenClassification,
+    OmniModelForSequenceRegression,
+    OmniModelForTokenRegression,
+    OmniModelForStructuralImputation,
+    OmniModelForMatrixRegression,
+    OmniModelForMatrixClassification,
+    OmniModelForMLM,
+    OmniModelForSeq2Seq,
+    OmniModelForRNADesign,
+    OmniModelForEmbedding,
+    OmniModelForAugmentation,
+)
+
+# Import LoRA model
+from .src.lora.lora_model import OmniLoraModel
+
+# Import tokenizer classes
+from .src.tokenizer import OmniBPETokenizer
+from .src.tokenizer import OmniKmersTokenizer
+from .src.tokenizer import OmniSingleNucleotideTokenizer
+
+# Import trainer classes
+from .src.trainer.hf_trainer import HFTrainer
+from .src.trainer.trainer import Trainer
+from .src.trainer.accelerate_trainer import AccelerateTrainer
+
+# Import hub utilities
+from .utility.hub_utils import download_benchmark
+from .utility.hub_utils import download_model
+from .utility.hub_utils import download_pipeline
+from .utility import hub_utils as hub_utils
+
+# Import hub classes
+from .utility.model_hub.model_hub import ModelHub
+from .utility.dataset_hub.dataset_hub import load_benchmark_datasets
+from .utility.pipeline_hub.pipeline import Pipeline
+from .utility.pipeline_hub.pipeline_hub import PipelineHub
+
+# Import module utilities
+from .src.model.module_utils import OmniPooling
+
+# --------------------------------------------------------------------------------
+# For backward compatibility version 0.2.7alpha and earlier
+from .src.abc.abstract_tokenizer import OmniTokenizer as OmniGenomeTokenizer
+from .src.abc.abstract_dataset import OmniDataset as OmniGenomeDataset
+from .src.abc.abstract_metric import OmniMetric as OmniGenomeMetric
+from .src.abc.abstract_model import OmniModel as OmniGenomeModel
+from .src.dataset.omni_dataset import OmniDatasetForSequenceClassification as OmniGenomeDatasetForSequenceClassification
+from .src.dataset.omni_dataset import OmniDatasetForSequenceRegression as OmniGenomeDatasetForSequenceRegression
+from .src.dataset.omni_dataset import OmniDatasetForTokenClassification as OmniGenomeDatasetForTokenClassification
+from .src.dataset.omni_dataset import OmniDatasetForTokenRegression as OmniGenomeDatasetForTokenRegression
+from .src.lora.lora_model import OmniLoraModel as OmniGenomeLoraModel
+from .src.model import (
+    OmniModelForSequenceClassification as OmniGenomeModelForSequenceClassification,
+    OmniModelForMultiLabelSequenceClassification as OmniGenomeModelForMultiLabelSequenceClassification,
+    OmniModelForTokenClassification as OmniGenomeModelForTokenClassification,
+    OmniModelForSequenceRegression as OmniGenomeModelForSequenceRegression,
+    OmniModelForTokenRegression as OmniGenomeModelForTokenRegression,
+    OmniModelForStructuralImputation as OmniGenomeModelForStructuralImputation,
+    OmniModelForMatrixRegression as OmniGenomeModelForMatrixRegression,
+    OmniModelForMatrixClassification as OmniGenomeModelForMatrixClassification,
+    OmniModelForMLM as OmniGenomeModelForMLM,
+    OmniModelForSeq2Seq as OmniGenomeModelForSeq2Seq,
+    OmniModelForRNADesign as OmniGenomeModelForRNADesign,
+    OmniModelForEmbedding as OmniGenomeModelForEmbedding,
+    OmniModelForAugmentation as OmniGenomeModelForAugmentation,
+
+)
+
+from .utility.ensemble import VoteEnsemblePredictor
+# ------------------------------------------------------------------------------
+
+
+__all__ = [
+    "load_benchmark_datasets",
+    "OmniDataset",
+    "OmniModel",
+    "OmniMetric",
+    "AutoTokenizer",
+    "OmniTokenizer",
+    "OmniKmersTokenizer",
+    "OmniSingleNucleotideTokenizer",
+    "OmniBPETokenizer",
+    "ModelHub",
+    "Pipeline",
+    "PipelineHub",
+    "BenchHub",
+    "AutoBench",
+    "AutoBenchConfig",
+    "utils",
+    "model",
+    "tokenizer",
+    "dataset",
+    "OmniModelForSequenceClassification",
+    "OmniModelForMultiLabelSequenceClassification",
+    "OmniModelForTokenClassification",
+    "OmniModelForSequenceRegression",
+    "OmniModelForTokenRegression",
+    "OmniModelForRNADesign",
+    "OmniModelForEmbedding",
+    "OmniModelForAugmentation",
+    "OmniModelForStructuralImputation",
+    "OmniModelForMatrixRegression",
+    "OmniModelForMatrixClassification",
+    "OmniModelForMLM",
+    "OmniModelForSeq2Seq",
+    "OmniDatasetForTokenClassification",
+    "OmniDatasetForTokenRegression",
+    "OmniDatasetForSequenceClassification",
+    "OmniDatasetForSequenceRegression",
+    "OmniLoraModel",
+    "ClassificationMetric",
+    "RegressionMetric",
+    "RankingMetric",
+    "Trainer",
+    "HFTrainer",
+    "AccelerateTrainer",
+    "AutoBenchConfig",
+    "AutoBench",
+    "download_benchmark",
+    "download_model",
+    "download_pipeline",
+    "VoteEnsemblePredictor"
+]
+
+
+LOGO1 = r"""                       
+    **@@ #========= @@**            ___                     _ 
+      **@@ +----- @@**             / _ \  _ __ ___   _ __  (_)
+        **@@ = @@**               | | | || '_ ` _ \ | '_ \ | |
+           **@@                   | |_| || | | | | || | | || |
+        @@** = **@@                \___/ |_| |_| |_||_| |_||_|
+     @@** ------+ **@@                
+   @@** =========# **@@            ____  
+  @@ ---------------+ @@          / ___|  ___  _ __    ___   _ __ ___    ___ 
+ @@ ================== @@        | |  _  / _ \| '_ \  / _ \ | '_ ` _ \  / _ \
+  @@ +--------------- @@         | |_| ||  __/| | | || (_) || | | | | ||  __/ 
+   @@** #========= **@@           \____| \___||_| |_| \___/ |_| |_| |_| \___| 
+    @@** +------ **@@          
+       @@** = **@@           
+          @@**                    ____                      _   
+       **@@ = @@**               | __ )   ___  _ __    ___ | |__  
+    **@@ -----+  @@**            |  _ \  / _ \| '_ \  / __|| '_ \ 
+  **@@ ==========# @@**          | |_) ||  __/| | | || (__ | | | |
+  @@ --------------+ @@**        |____/  \___||_| |_| \___||_| |_|
+"""
+
+LOGO2 = r"""
+
+   **  +----------- **           ___                     _ 
+  @@                 @@         / _ \  _ __ ___   _ __  (_)
+ @@* #============== *@@       | | | || '_ ` _ \ | '_ \ | |
+ @@*                 *@@       | |_| || | | | | || | | || |
+ *@@  +------------ *@@         \___/ |_| |_| |_||_| |_||_|
+  *@*               @@*       
+   *@@  #========= @@*        
+    *@@*         *@@*          
+      *@@  +---@@@*              ____  
+        *@@*   **               / ___|  ___  _ __    ___   _ __ ___    ___ 
+          **@**                | |  _  / _ \| '_ \  / _ \ | '_ ` _ \  / _ \ 
+        *@@* *@@*              | |_| ||  __/| | | || (_) || | | | | ||  __/ 
+      *@@ ---+  @@*             \____| \___||_| |_| \___/ |_| |_| |_| \___| 
+    *@@*         *@@*          
+   *@@ =========#  @@*         
+  *@@               @@*        
+ *@@ -------------+  @@*        ____                      _   
+ @@                   @@       | __ )   ___  _ __    ___ | |__ 
+ @@ ===============#  @@       |  _ \  / _ \| '_ \  / __|| '_ \ 
+  @@                 @@        | |_) ||  __/| | | || (__ | | | |
+   ** -----------+  **         |____/  \___||_| |_| \___||_| |_|
+"""
+
+art_dna_color_map = {
+    "*": "blue",  # Bases represented by '*'
+    "@": "white",  # Bases represented by '@'
+    "-": "yellow",  # Hydrogen bonds, assuming '-' represents a bond
+    "=": "light_cyan",  # Hydrogen bonds, assuming '=' represents a bond
+    "+": "yellow",  # '+' symbols in cyan
+    " ": "black",  # Use red for undefined characters
+}
+import random
+
+LOGO = random.choice([LOGO1, LOGO2])
+print(LOGO)
+
+clean_temp_dir_pt_files()

omnigenome/auto/__init__.py

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+"""
+This package contains modules for automated processes such as benchmarking and training.
+"""

omnigenome/auto/auto_bench/__init__.py

@@ -0,0 +1,12 @@
+# -*- coding: utf-8 -*-
+# file: __init__.py
+# time: 18:28 11/04/2024
+# author: YANG, HENG <hy345@exeter.ac.uk> (杨恒)
+# github: https://github.com/yangheng95
+# huggingface: https://huggingface.co/yangheng
+# google scholar: https://scholar.google.com/citations?user=NPq5a_0AAAAJ&hl=en
+# Copyright (C) 2019-2024. All Rights Reserved.
+"""
+This package contains modules for automated benchmarking of models.
+"""
+