harmonizome 1.0.0__tar.gz

harmonizome-1.0.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be added to the global gitignore or merged into this project gitignore.  For a PyCharm
+#  project, uncomment the following line:
+#.idea/
+
+# Harmonizome specific
+# Downloaded datasets
+ENCODE/
+GTEx/
+MSigDB/
+# ... other dataset directories
+
+# Temporary files
+*.tmp
+*.temp 
+
+# Cache
+.harmonizome_cache/

harmonizome-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Shaurita D. Hutchins
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE. 

harmonizome-1.0.0/MANIFEST.in

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+include README.md
+include LICENSE
+include requirements.txt
+include pyproject.toml
+recursive-include tests *.py
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co] 

harmonizome-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: harmonizome
+Version: 1.0.0
+Summary: Python client for the Harmonizome API - a resource for exploring gene sets and their attributes
+Author-email: "Shaurita D. Hutchins" <shaurita.d.hutchins@gmail.com>
+Maintainer-email: "Shaurita D. Hutchins" <shaurita.d.hutchins@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://maayanlab.cloud/Harmonizome/
+Project-URL: Documentation, https://maayanlab.cloud/Harmonizome/
+Project-URL: Repository, https://github.com/sdhutchins/harmonizome
+Project-URL: Bug Tracker, https://github.com/sdhutchins/harmonizome/issues
+Keywords: bioinformatics,genomics,gene-sets,harmonizome,api-client
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.19.0
+Requires-Dist: pandas>=1.3.0
+Requires-Dist: scipy>=1.7.0
+Provides-Extra: dev
+Requires-Dist: pytest>=6.0; extra == "dev"
+Requires-Dist: pytest-cov>=2.0; extra == "dev"
+Requires-Dist: black>=21.0; extra == "dev"
+Requires-Dist: isort>=5.0; extra == "dev"
+Requires-Dist: flake8>=3.8; extra == "dev"
+Dynamic: license-file
+
+# Harmonizome Python Client
+
+A Python client for the [Harmonizome API](https://maayanlab.cloud/Harmonizome/), a resource for exploring gene sets and their attributes across multiple datasets.
+
+## Installation
+
+```bash
+pip install harmonizome
+```
+
+## Quick Start
+
+```python
+from harmonizome import Harmonizome
+
+# Get all available datasets
+datasets = Harmonizome.DATASETS
+print(f"Available datasets: {len(datasets)}")
+
+# Get information about a specific gene
+gene_info = Harmonizome.get('gene', 'BRCA1')
+print(f"Gene: {gene_info['name']}")
+
+# Download data for a specific dataset
+for filename in Harmonizome.download(['ENCODE']):
+    print(f"Downloaded: {filename}")
+
+# Load data as pandas DataFrames
+for df in Harmonizome.download_df(['ENCODE'], sparse=False):
+    print(f"DataFrame shape: {df.shape}")
+```
+
+## Features
+
+- **API Access**: Query genes, gene sets, attributes, and datasets
+- **Data Download**: Download complete datasets (~30GB total)
+- **DataFrame Support**: Load data directly as pandas DataFrames
+- **Sparse Matrix Support**: Efficient handling of large sparse datasets
+- **Python 2/3 Compatibility**: Works with both Python 2.X and 3.X
+
+## API Reference
+
+### Core Methods
+
+#### `Harmonizome.get(entity, name=None, start_at=None)`
+Retrieve entities from the Harmonizome API.
+
+- `entity`: Type of entity ('gene', 'gene_set', 'attribute', etc.)
+- `name`: Specific entity name (optional)
+- `start_at`: Cursor position for pagination (optional)
+
+#### `Harmonizome.download(datasets=None, what=None)`
+Download dataset files to local directories.
+
+- `datasets`: List of dataset names (defaults to all datasets)
+- `what`: List of file types to download (defaults to all types)
+
+#### `Harmonizome.download_df(datasets=None, what=None, sparse=False)`
+Download and load data as pandas DataFrames.
+
+- `datasets`: List of dataset names
+- `what`: List of file types to download
+- `sparse`: Use sparse matrices for memory efficiency
+
+### Entity Types
+
+- `DATASET`: Dataset information
+- `GENE`: Gene information
+- `GENE_SET`: Gene set collections
+- `ATTRIBUTE`: Gene attributes
+- `GENE_FAMILY`: Gene family classifications
+- `NAMING_AUTHORITY`: Naming authorities
+- `PROTEIN`: Protein information
+- `RESOURCE`: Data resources
+
+## Examples
+
+### Querying Genes
+
+```python
+# Get all genes (paginated)
+genes = Harmonizome.get('gene')
+print(f"Found {len(genes['entities'])} genes")
+
+# Get next page
+next_genes = Harmonizome.next(genes)
+
+# Get specific gene
+brca1 = Harmonizome.get('gene', 'BRCA1')
+print(f"BRCA1 description: {brca1['description']}")
+```
+
+### Downloading Datasets
+
+```python
+# Download all data (requires confirmation)
+for filename in Harmonizome.download():
+    print(f"Downloaded: {filename}")
+
+# Download specific datasets
+datasets = ['ENCODE', 'GTEx']
+for filename in Harmonizome.download(datasets):
+    print(f"Downloaded: {filename}")
+
+# Download specific file types
+file_types = ['gene_attribute_matrix.txt.gz']
+for filename in Harmonizome.download(['ENCODE'], file_types):
+    print(f"Downloaded: {filename}")
+```
+
+### Working with DataFrames
+
+```python
+# Load as regular DataFrames
+for df in Harmonizome.download_df(['ENCODE']):
+    print(f"DataFrame: {df.shape}")
+    print(f"Columns: {df.columns[:5].tolist()}")
+    break
+
+# Load as sparse DataFrames (memory efficient)
+for df in Harmonizome.download_df(['ENCODE'], sparse=True):
+    print(f"Sparse DataFrame: {df.shape}")
+    print(f"Memory usage: {df.memory_usage(deep=True).sum() / 1024**2:.2f} MB")
+    break
+```
+
+### Working with Gene Associations as DataFrames
+
+You can fetch all associations for a gene and convert them directly to a pandas DataFrame for easy filtering and export:
+
+```python
+from harmonizome import Harmonizome
+
+gene = "STAT3"
+gene_data = Harmonizome.get_gene_data(gene, use_cache=True)
+
+# Get all associations as a DataFrame
+df = gene_data.to_dataframe()
+
+# List all unique dataset names
+print("Available datasets for this gene:")
+for i, dataset in enumerate(df["dataset"].unique(), 1):
+    print(f"{i}. {dataset}")
+
+# Select a dataset by name
+selected_dataset = df["dataset"].unique()[0]  # or set to any dataset name from the list
+print(f"\nSelected dataset: {selected_dataset}")
+
+# Filter associations for the selected dataset
+dataset_df = df[df["dataset"] == selected_dataset]
+print(dataset_df)
+
+# Save to CSV
+safe_name = selected_dataset.replace(" ", "_").replace("/", "_")
+dataset_df.to_csv(f"{gene.lower()}_{safe_name}_associations.csv", index=False)
+```
+
+### API Reference: GeneData.to_dataframe()
+
+```python
+gene_data.to_dataframe(dataset: str = None) -> pandas.DataFrame
+```
+- Returns a DataFrame with columns: 'gene_set', 'dataset', 'thresholdValue', 'standardizedValue'.
+- Optionally filter by dataset name.
+
+## File Types
+
+The following file types are available for download:
+
+- `gene_attribute_matrix.txt.gz`: Gene-attribute association matrix
+- `gene_list_terms.txt.gz`: List of genes with terms
+- `attribute_list_entries.txt.gz`: List of attributes with entries
+
+## Requirements
+
+- Python 3.7+
+- numpy >= 1.19.0
+- pandas >= 1.3.0
+- scipy >= 1.7.0
+
+## Development
+
+```bash
+# Install development dependencies
+pip install -e .
+
+# Run tests
+pytest
+```
+
+## License
+
+This project is licensed under the [MIT License](LICENSE).
+
+## Citation
+
+If you use this package in your research, please cite:
+
+```
+Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma'ayan A. The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database (Oxford). 2016 Jul 3;2016:baw100. doi: 10.1093/database/baw100.
+```
+
+## Links
+
+- [Harmonizome Website](https://maayanlab.cloud/Harmonizome/)
+- [API Documentation](https://maayanlab.cloud/Harmonizome/api)
+- [GitHub Repository](https://github.com/maayanlab/harmonizome) 

harmonizome-1.0.0/README.md

@@ -0,0 +1,207 @@
+# Harmonizome Python Client
+
+A Python client for the [Harmonizome API](https://maayanlab.cloud/Harmonizome/), a resource for exploring gene sets and their attributes across multiple datasets.
+
+## Installation
+
+```bash
+pip install harmonizome
+```
+
+## Quick Start
+
+```python
+from harmonizome import Harmonizome
+
+# Get all available datasets
+datasets = Harmonizome.DATASETS
+print(f"Available datasets: {len(datasets)}")
+
+# Get information about a specific gene
+gene_info = Harmonizome.get('gene', 'BRCA1')
+print(f"Gene: {gene_info['name']}")
+
+# Download data for a specific dataset
+for filename in Harmonizome.download(['ENCODE']):
+    print(f"Downloaded: {filename}")
+
+# Load data as pandas DataFrames
+for df in Harmonizome.download_df(['ENCODE'], sparse=False):
+    print(f"DataFrame shape: {df.shape}")
+```
+
+## Features
+
+- **API Access**: Query genes, gene sets, attributes, and datasets
+- **Data Download**: Download complete datasets (~30GB total)
+- **DataFrame Support**: Load data directly as pandas DataFrames
+- **Sparse Matrix Support**: Efficient handling of large sparse datasets
+- **Python 2/3 Compatibility**: Works with both Python 2.X and 3.X
+
+## API Reference
+
+### Core Methods
+
+#### `Harmonizome.get(entity, name=None, start_at=None)`
+Retrieve entities from the Harmonizome API.
+
+- `entity`: Type of entity ('gene', 'gene_set', 'attribute', etc.)
+- `name`: Specific entity name (optional)
+- `start_at`: Cursor position for pagination (optional)
+
+#### `Harmonizome.download(datasets=None, what=None)`
+Download dataset files to local directories.
+
+- `datasets`: List of dataset names (defaults to all datasets)
+- `what`: List of file types to download (defaults to all types)
+
+#### `Harmonizome.download_df(datasets=None, what=None, sparse=False)`
+Download and load data as pandas DataFrames.
+
+- `datasets`: List of dataset names
+- `what`: List of file types to download
+- `sparse`: Use sparse matrices for memory efficiency
+
+### Entity Types
+
+- `DATASET`: Dataset information
+- `GENE`: Gene information
+- `GENE_SET`: Gene set collections
+- `ATTRIBUTE`: Gene attributes
+- `GENE_FAMILY`: Gene family classifications
+- `NAMING_AUTHORITY`: Naming authorities
+- `PROTEIN`: Protein information
+- `RESOURCE`: Data resources
+
+## Examples
+
+### Querying Genes
+
+```python
+# Get all genes (paginated)
+genes = Harmonizome.get('gene')
+print(f"Found {len(genes['entities'])} genes")
+
+# Get next page
+next_genes = Harmonizome.next(genes)
+
+# Get specific gene
+brca1 = Harmonizome.get('gene', 'BRCA1')
+print(f"BRCA1 description: {brca1['description']}")
+```
+
+### Downloading Datasets
+
+```python
+# Download all data (requires confirmation)
+for filename in Harmonizome.download():
+    print(f"Downloaded: {filename}")
+
+# Download specific datasets
+datasets = ['ENCODE', 'GTEx']
+for filename in Harmonizome.download(datasets):
+    print(f"Downloaded: {filename}")
+
+# Download specific file types
+file_types = ['gene_attribute_matrix.txt.gz']
+for filename in Harmonizome.download(['ENCODE'], file_types):
+    print(f"Downloaded: {filename}")
+```
+
+### Working with DataFrames
+
+```python
+# Load as regular DataFrames
+for df in Harmonizome.download_df(['ENCODE']):
+    print(f"DataFrame: {df.shape}")
+    print(f"Columns: {df.columns[:5].tolist()}")
+    break
+
+# Load as sparse DataFrames (memory efficient)
+for df in Harmonizome.download_df(['ENCODE'], sparse=True):
+    print(f"Sparse DataFrame: {df.shape}")
+    print(f"Memory usage: {df.memory_usage(deep=True).sum() / 1024**2:.2f} MB")
+    break
+```
+
+### Working with Gene Associations as DataFrames
+
+You can fetch all associations for a gene and convert them directly to a pandas DataFrame for easy filtering and export:
+
+```python
+from harmonizome import Harmonizome
+
+gene = "STAT3"
+gene_data = Harmonizome.get_gene_data(gene, use_cache=True)
+
+# Get all associations as a DataFrame
+df = gene_data.to_dataframe()
+
+# List all unique dataset names
+print("Available datasets for this gene:")
+for i, dataset in enumerate(df["dataset"].unique(), 1):
+    print(f"{i}. {dataset}")
+
+# Select a dataset by name
+selected_dataset = df["dataset"].unique()[0]  # or set to any dataset name from the list
+print(f"\nSelected dataset: {selected_dataset}")
+
+# Filter associations for the selected dataset
+dataset_df = df[df["dataset"] == selected_dataset]
+print(dataset_df)
+
+# Save to CSV
+safe_name = selected_dataset.replace(" ", "_").replace("/", "_")
+dataset_df.to_csv(f"{gene.lower()}_{safe_name}_associations.csv", index=False)
+```
+
+### API Reference: GeneData.to_dataframe()
+
+```python
+gene_data.to_dataframe(dataset: str = None) -> pandas.DataFrame
+```
+- Returns a DataFrame with columns: 'gene_set', 'dataset', 'thresholdValue', 'standardizedValue'.
+- Optionally filter by dataset name.
+
+## File Types
+
+The following file types are available for download:
+
+- `gene_attribute_matrix.txt.gz`: Gene-attribute association matrix
+- `gene_list_terms.txt.gz`: List of genes with terms
+- `attribute_list_entries.txt.gz`: List of attributes with entries
+
+## Requirements
+
+- Python 3.7+
+- numpy >= 1.19.0
+- pandas >= 1.3.0
+- scipy >= 1.7.0
+
+## Development
+
+```bash
+# Install development dependencies
+pip install -e .
+
+# Run tests
+pytest
+```
+
+## License
+
+This project is licensed under the [MIT License](LICENSE).
+
+## Citation
+
+If you use this package in your research, please cite:
+
+```
+Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma'ayan A. The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database (Oxford). 2016 Jul 3;2016:baw100. doi: 10.1093/database/baw100.
+```
+
+## Links
+
+- [Harmonizome Website](https://maayanlab.cloud/Harmonizome/)
+- [API Documentation](https://maayanlab.cloud/Harmonizome/api)
+- [GitHub Repository](https://github.com/maayanlab/harmonizome) 

harmonizome-1.0.0/examples/__init__.py

@@ -0,0 +1 @@
+"""Examples package for harmonizome.""" 

harmonizome-1.0.0/examples/dataset_query.py

@@ -0,0 +1,20 @@
+from harmonizome import Harmonizome
+
+gene = "STAT3"
+gene_data = Harmonizome.get_gene_data(gene, use_cache=True)
+
+# Get all associations as a DataFrame
+df = gene_data.to_dataframe()
+
+# Example: select a dataset by name (replace with your choice)
+selected_dataset = df["dataset"].unique()[0]  # or set to any dataset name from the list
+print(f"\nSelected dataset: {selected_dataset}")
+
+# Filter associations for the selected dataset
+dataset_df = df[df["dataset"] == selected_dataset]
+print(dataset_df)
+
+# Save to CSV
+safe_name = selected_dataset.replace(" ", "_").replace("/", "_")
+dataset_df.to_csv(f"{gene.lower()}_{safe_name}_associations.csv", index=False)
+print(f"Saved {len(dataset_df)} associations for dataset '{selected_dataset}' to {gene.lower()}_{safe_name}_associations.csv")

harmonizome-1.0.0/harmonizome/__init__.py

@@ -0,0 +1,6 @@
+"""Harmonizome Python Client - A resource for exploring gene sets and their attributes."""
+
+from .harmonizome import Harmonizome, Entity, VERSION
+
+__version__ = VERSION
+__all__ = ['Harmonizome', 'Entity', 'VERSION']