pyrna-lab 0.1.0__tar.gz

pyrna_lab-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pyrna-lab
+Version: 0.1.0
+Summary: An open-source Python toolkit for RNA analysis and AI research.
+Author: Mohammad Paknahad
+Maintainer: Mohammad Paknahad
+License: MIT
+Project-URL: Homepage, https://github.com/paknahad91/PyRNA-Lab
+Project-URL: Repository, https://github.com/paknahad91/PyRNA-Lab
+Project-URL: Issues, https://github.com/MohammadPaknahad/PyRNA-Lab/issues
+Keywords: RNA,bioinformatics,machine-learning,deep-learning,RNA-structure,computational-biology
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=1.26
+Requires-Dist: pandas>=2.0
+Provides-Extra: ai
+Requires-Dist: torch>=2.0; extra == "ai"
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0; extra == "dev"
+Requires-Dist: build>=1.0; extra == "dev"
+Requires-Dist: twine>=5.0; extra == "dev"
+
+# PyRNA-Lab 🧬
+
+PyRNA-Lab is an open-source Python toolkit for RNA analysis,
+machine learning, and computational biology research.
+
+## Vision
+
+Our goal is to build a reproducible and accessible computational
+laboratory for RNA research.
+
+PyRNA-Lab will provide tools for:
+
+- RNA sequence analysis
+- Data preprocessing
+- RNA structure analysis
+- Machine learning
+- Deep learning
+- Prediction
+- Model evaluation
+- Visualization
+- Explainability
+- Uncertainty estimation
+
+
+Mohammad Paknahad (c)
+2026

pyrna_lab-0.1.0/README.md

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+# PyRNA-Lab 🧬
+
+PyRNA-Lab is an open-source Python toolkit for RNA analysis,
+machine learning, and computational biology research.
+
+## Vision
+
+Our goal is to build a reproducible and accessible computational
+laboratory for RNA research.
+
+PyRNA-Lab will provide tools for:
+
+- RNA sequence analysis
+- Data preprocessing
+- RNA structure analysis
+- Machine learning
+- Deep learning
+- Prediction
+- Model evaluation
+- Visualization
+- Explainability
+- Uncertainty estimation
+
+
+Mohammad Paknahad (c)
+2026

pyrna_lab-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=68"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pyrna-lab"
+version = "0.1.0"
+description = "An open-source Python toolkit for RNA analysis and AI research."
+readme = "README.md"
+requires-python = ">=3.10"
+license = { text = "MIT" }
+
+authors = [
+    { name = "Mohammad Paknahad" }
+]
+
+maintainers = [
+    { name = "Mohammad Paknahad" }
+]
+
+keywords = [
+    "RNA",
+    "bioinformatics",
+    "machine-learning",
+    "deep-learning",
+    "RNA-structure",
+    "computational-biology"
+]
+
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Bio-Informatics"
+]
+
+dependencies = [
+    "numpy>=1.26",
+    "pandas>=2.0"
+]
+
+[project.optional-dependencies]
+ai = [
+    "torch>=2.0"
+]
+
+dev = [
+    "pytest>=8.0",
+    "build>=1.0",
+    "twine>=5.0"
+]
+
+[project.urls]
+Homepage = "https://github.com/paknahad91/PyRNA-Lab"
+Repository = "https://github.com/paknahad91/PyRNA-Lab"
+Issues = "https://github.com/MohammadPaknahad/PyRNA-Lab/issues"
+
+
+[tool.setuptools.packages.find]
+where = ["."]
+
+[tool.setuptools.package-data]
+rna_lab = ["*.pth"]

pyrna_lab-0.1.0/pyrna_lab.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: pyrna-lab
+Version: 0.1.0
+Summary: An open-source Python toolkit for RNA analysis and AI research.
+Author: Mohammad Paknahad
+Maintainer: Mohammad Paknahad
+License: MIT
+Project-URL: Homepage, https://github.com/paknahad91/PyRNA-Lab
+Project-URL: Repository, https://github.com/paknahad91/PyRNA-Lab
+Project-URL: Issues, https://github.com/MohammadPaknahad/PyRNA-Lab/issues
+Keywords: RNA,bioinformatics,machine-learning,deep-learning,RNA-structure,computational-biology
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=1.26
+Requires-Dist: pandas>=2.0
+Provides-Extra: ai
+Requires-Dist: torch>=2.0; extra == "ai"
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0; extra == "dev"
+Requires-Dist: build>=1.0; extra == "dev"
+Requires-Dist: twine>=5.0; extra == "dev"
+
+# PyRNA-Lab 🧬
+
+PyRNA-Lab is an open-source Python toolkit for RNA analysis,
+machine learning, and computational biology research.
+
+## Vision
+
+Our goal is to build a reproducible and accessible computational
+laboratory for RNA research.
+
+PyRNA-Lab will provide tools for:
+
+- RNA sequence analysis
+- Data preprocessing
+- RNA structure analysis
+- Machine learning
+- Deep learning
+- Prediction
+- Model evaluation
+- Visualization
+- Explainability
+- Uncertainty estimation
+
+
+Mohammad Paknahad (c)
+2026

pyrna_lab-0.1.0/pyrna_lab.egg-info/SOURCES.txt

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+README.md
+pyproject.toml
+pyrna_lab.egg-info/PKG-INFO
+pyrna_lab.egg-info/SOURCES.txt
+pyrna_lab.egg-info/dependency_links.txt
+pyrna_lab.egg-info/requires.txt
+pyrna_lab.egg-info/top_level.txt
+rna_lab/__init__.py
+rna_lab/ai_dataset.py
+rna_lab/app.py
+rna_lab/baseline_paired_unpaired.pth
+rna_lab/dataset.py
+rna_lab/evaluate.py
+rna_lab/evaluate_pair.py
+rna_lab/evaluate_pair2.py
+rna_lab/model.py
+rna_lab/pair_model.py
+rna_lab/predict.py
+rna_lab/preprocessing.py
+rna_lab/rna_model.pth
+rna_lab/rna_pair_model.pth
+rna_lab/sequence.py
+rna_lab/structure.py
+rna_lab/test_pair_model.py
+rna_lab/test_real_data.py
+rna_lab/train.py
+rna_lab/train_pair.py
+rna_lab/train_pair_full.py
+rna_lab/validation.py

pyrna_lab-0.1.0/pyrna_lab.egg-info/dependency_links.txt

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+

pyrna_lab-0.1.0/pyrna_lab.egg-info/requires.txt

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+numpy>=1.26
+pandas>=2.0
+
+[ai]
+torch>=2.0
+
+[dev]
+pytest>=8.0
+build>=1.0
+twine>=5.0

pyrna_lab-0.1.0/pyrna_lab.egg-info/top_level.txt

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+dist
+rna_lab

pyrna_lab-0.1.0/rna_lab/__init__.py

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+"""
+PyRNA-Lab
+
+An open-source Python toolkit for RNA analysis and AI research.
+
+in the name of GOD
+
+Mohammad Paknahad from IRAN
+
+"""
+
+__version__ = "0.1.0"
+
+__author__ = "Mohammad Paknahad"
+
+__name__ = "PyRNA-Lab"

pyrna_lab-0.1.0/rna_lab/ai_dataset.py

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+from dataset import EFoldDataset
+from preprocessing import preprocess_record
+
+
+DATASET_PATH = "doi_10_5061_dryad_79cnp5j95__v20260129/efold_train.json"
+
+
+class RNAAIDataset:
+    def __init__(self, file_path):
+        self.dataset = EFoldDataset(file_path)
+
+    def samples(self, limit=10):
+        count = 0
+
+        for name, record in self.dataset:
+            encoded, target = preprocess_record(record)
+
+            yield {
+                "name": name,
+                "sequence": encoded,
+                "target": target
+            }
+
+            count += 1
+
+            if count == limit:
+                break
+
+
+if __name__ == "__main__":
+    dataset = RNAAIDataset(DATASET_PATH)
+
+    for sample in dataset.samples(3):
+        print("=" * 50)
+        print("RNA:", sample["name"])
+        print("Input length:", len(sample["sequence"]))
+        print("Target length:", len(sample["target"]))
+        print("Input:", sample["sequence"])
+        print("Target:", sample["target"])