de-quack 0.1.0__tar.gz

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  1. de_quack-0.1.0/LICENSE +21 -0
  2. de_quack-0.1.0/PKG-INFO +110 -0
  3. de_quack-0.1.0/README.md +80 -0
  4. de_quack-0.1.0/pyproject.toml +46 -0
  5. de_quack-0.1.0/setup.cfg +4 -0
  6. de_quack-0.1.0/src/de_quack.egg-info/PKG-INFO +110 -0
  7. de_quack-0.1.0/src/de_quack.egg-info/SOURCES.txt +8 -0
  8. de_quack-0.1.0/src/de_quack.egg-info/dependency_links.txt +1 -0
  9. de_quack-0.1.0/src/de_quack.egg-info/requires.txt +8 -0
  10. de_quack-0.1.0/src/de_quack.egg-info/top_level.txt +1 -0
de_quack-0.1.0/LICENSE ADDED
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+ MIT License
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+
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+ Copyright (c) 2026 Ziyang Xing
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
de_quack-0.1.0/PKG-INFO ADDED
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+ Metadata-Version: 2.4
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+ Name: de_quack
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+ Version: 0.1.0
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+ Summary: Python library for differential expression data storage and visualization using DuckDB.
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+ Author: yangp7833-commits
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+ License: MIT
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+ Keywords: duckdb,differential expression,bioinformatics,visualization,data management
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: Programming Language :: Python :: 3.8
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+ Classifier: Programming Language :: Python :: 3.9
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+ Classifier: Programming Language :: Python :: 3.10
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+ Classifier: Programming Language :: Python :: 3.11
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+ Classifier: Programming Language :: Python :: 3.12
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+ Classifier: Programming Language :: Python :: 3.13
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+ Classifier: License :: OSI Approved :: MIT License
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+ Classifier: Operating System :: OS Independent
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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+ Requires-Python: >=3.9
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+ Description-Content-Type: text/markdown
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+ License-File: LICENSE
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+ Requires-Dist: duckdb>=1.0
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+ Requires-Dist: pandas>=1.0
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+ Requires-Dist: numpy>=1.20
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+ Requires-Dist: matplotlib>=3.0
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+ Requires-Dist: adjustText>=0.7
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+ Provides-Extra: excel
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+ Requires-Dist: openpyxl>=3.0; extra == "excel"
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+ Dynamic: license-file
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+
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+ # de_quack
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+
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+ Python/R library for differential expression (DE) data management and visualization using DuckDB.
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+
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+ Stores DE analysis results with automatic gene annotation, enabling reproducible and efficient querying of experimental data.
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+
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+ ## Features
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+
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+ - **Efficient Storage**: DuckDB-backed persistence for gene expression results
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+ - **Automatic Annotation**: Maps gene symbols and Ensembl IDs with canonical references
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+ - **Flexible Querying**: Filter results using simple keyword arguments (e.g., `padj__lt=0.05`)
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+ - **Multi-language Support**: Native Python and R interfaces
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+ - **Visualization**: Built-in volcano plot generation with publication-ready styling
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+ - **Data Normalization**: Handles variable column names and formats automatically
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+
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+ ## Installation
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+
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+ ```bash
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+ pip install de_quack
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+ ```
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+
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+ For Excel export support (optional):
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+ ```bash
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+ pip install de_quack[excel]
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+ ```
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+
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+ ## Quick Start
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+
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+ ### Python
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+
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+ ```python
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+ from de_quack import de_duckling, volcano_plot
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+
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+ with de_duckling('results.duckdb') as db:
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+ db.initialize_gene_table('human')
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+ db.insert_to_database('data.txt')
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+ results = db.query('gene_results', padj__lt=0.05)
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+ print(results)
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+
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+ # Generate volcano plot
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+ volcano_plot(results, padj=0.05, log2fc=1, plot_file='volcano.png')
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+ ```
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+
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+ ### R
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+
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+ ```r
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+ # Find and source the wrapper directly from the pip installation directory
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+ py_pkg_path <- dirname(reticulate::import("de_quack")$`__file__`)
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+ source(file.path(py_pkg_path, "wrapper.R"))
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+
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+ # Initialize
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+ duck <- de_quack(db_path = "results.duckdb")
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+ duck$connect()
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+ duck$initialize_gene_table('human')
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+ duck$insert_to_database('data.txt')
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+ results <- duck$query('gene_results', padj__lt=0.05)
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+ duck$volcano_plot(results, padj=0.05, log2fc=1, plot_file='volcano.png')
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+ duck$close()
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+ ```
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+
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+ ## Database Schema
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+
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+ ### Tables
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+
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+ - **experimental_data**: Metadata about DE analysis experiments
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+ - **gene_results**: Individual gene-level results with statistics
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+ - **genes**: Reference gene annotations (human, etc.)
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+
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+ ### Advanced Querying & JSON Fallback
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+ DeDuck supports intuitive field modifiers (`__lt`, `__gt`, `__lte`, `__gte`, `__ne`). If a metric isn't a native column in the database, DeDuck automatically queries it out of custom nested JSON metadata dynamically:
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+
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+ ```python
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+ # Regular column filtering + automatic nested JSON key metadata extraction
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+ with de_duckling as db:
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+ results = db.query('gene_results', padj__lt=0.05, custom_biotype__ne='pseudogene')
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+ ```
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+
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+ ## License
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+
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+ MIT
de_quack-0.1.0/README.md ADDED
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+ # de_quack
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+
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+ Python/R library for differential expression (DE) data management and visualization using DuckDB.
4
+
5
+ Stores DE analysis results with automatic gene annotation, enabling reproducible and efficient querying of experimental data.
6
+
7
+ ## Features
8
+
9
+ - **Efficient Storage**: DuckDB-backed persistence for gene expression results
10
+ - **Automatic Annotation**: Maps gene symbols and Ensembl IDs with canonical references
11
+ - **Flexible Querying**: Filter results using simple keyword arguments (e.g., `padj__lt=0.05`)
12
+ - **Multi-language Support**: Native Python and R interfaces
13
+ - **Visualization**: Built-in volcano plot generation with publication-ready styling
14
+ - **Data Normalization**: Handles variable column names and formats automatically
15
+
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+ ## Installation
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+
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+ ```bash
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+ pip install de_quack
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+ ```
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+
22
+ For Excel export support (optional):
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+ ```bash
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+ pip install de_quack[excel]
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+ ```
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+
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+ ## Quick Start
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+
29
+ ### Python
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+
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+ ```python
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+ from de_quack import de_duckling, volcano_plot
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+
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+ with de_duckling('results.duckdb') as db:
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+ db.initialize_gene_table('human')
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+ db.insert_to_database('data.txt')
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+ results = db.query('gene_results', padj__lt=0.05)
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+ print(results)
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+
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+ # Generate volcano plot
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+ volcano_plot(results, padj=0.05, log2fc=1, plot_file='volcano.png')
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+ ```
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+
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+ ### R
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+
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+ ```r
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+ # Find and source the wrapper directly from the pip installation directory
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+ py_pkg_path <- dirname(reticulate::import("de_quack")$`__file__`)
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+ source(file.path(py_pkg_path, "wrapper.R"))
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+
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+ # Initialize
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+ duck <- de_quack(db_path = "results.duckdb")
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+ duck$connect()
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+ duck$initialize_gene_table('human')
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+ duck$insert_to_database('data.txt')
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+ results <- duck$query('gene_results', padj__lt=0.05)
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+ duck$volcano_plot(results, padj=0.05, log2fc=1, plot_file='volcano.png')
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+ duck$close()
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+ ```
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+
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+ ## Database Schema
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+
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+ ### Tables
64
+
65
+ - **experimental_data**: Metadata about DE analysis experiments
66
+ - **gene_results**: Individual gene-level results with statistics
67
+ - **genes**: Reference gene annotations (human, etc.)
68
+
69
+ ### Advanced Querying & JSON Fallback
70
+ DeDuck supports intuitive field modifiers (`__lt`, `__gt`, `__lte`, `__gte`, `__ne`). If a metric isn't a native column in the database, DeDuck automatically queries it out of custom nested JSON metadata dynamically:
71
+
72
+ ```python
73
+ # Regular column filtering + automatic nested JSON key metadata extraction
74
+ with de_duckling as db:
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+ results = db.query('gene_results', padj__lt=0.05, custom_biotype__ne='pseudogene')
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+ ```
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+
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+ ## License
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+
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+ MIT
de_quack-0.1.0/pyproject.toml ADDED
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+ [build-system]
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+ requires = ["setuptools>=61.0", "wheel"]
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+ build-backend = "setuptools.build_meta"
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+
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+ [project]
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+ name = "de_quack"
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+ version = "0.1.0"
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+ description = "Python library for differential expression data storage and visualization using DuckDB."
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+ readme = "README.md"
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+ requires-python = ">=3.9"
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+ license = { text = "MIT" }
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+ keywords = ["duckdb", "differential expression", "bioinformatics", "visualization", "data management"]
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+ authors = [
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+ { name = "yangp7833-commits" }
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+ ]
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+ classifiers = [
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+ "Programming Language :: Python :: 3",
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+ "Programming Language :: Python :: 3.8",
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+ "Programming Language :: Python :: 3.9",
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+ "Programming Language :: Python :: 3.10",
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+ "Programming Language :: Python :: 3.11",
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+ "Programming Language :: Python :: 3.12",
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+ "Programming Language :: Python :: 3.13",
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+ "License :: OSI Approved :: MIT License",
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+ "Operating System :: OS Independent",
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+ "Intended Audience :: Science/Research",
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+ "Topic :: Scientific/Engineering :: Bio-Informatics"
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+ ]
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+
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+ dependencies = [
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+ "duckdb>=1.0",
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+ "pandas>=1.0",
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+ "numpy>=1.20",
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+ "matplotlib>=3.0",
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+ "adjustText>=0.7"
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+ ]
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+
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+ [project.optional-dependencies]
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+ excel = ["openpyxl>=3.0"]
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+
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+ [tool.setuptools.packages.find]
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+ where = ["src"]
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+ include = ["de_duck*"]
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+
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+ [tool.setuptools.package-data]
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+ "*" = ["*.py"]
de_quack-0.1.0/setup.cfg ADDED
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+ [egg_info]
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+ tag_build =
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+ tag_date = 0
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+
de_quack-0.1.0/src/de_quack.egg-info/PKG-INFO ADDED
@@ -0,0 +1,110 @@
1
+ Metadata-Version: 2.4
2
+ Name: de_quack
3
+ Version: 0.1.0
4
+ Summary: Python library for differential expression data storage and visualization using DuckDB.
5
+ Author: yangp7833-commits
6
+ License: MIT
7
+ Keywords: duckdb,differential expression,bioinformatics,visualization,data management
8
+ Classifier: Programming Language :: Python :: 3
9
+ Classifier: Programming Language :: Python :: 3.8
10
+ Classifier: Programming Language :: Python :: 3.9
11
+ Classifier: Programming Language :: Python :: 3.10
12
+ Classifier: Programming Language :: Python :: 3.11
13
+ Classifier: Programming Language :: Python :: 3.12
14
+ Classifier: Programming Language :: Python :: 3.13
15
+ Classifier: License :: OSI Approved :: MIT License
16
+ Classifier: Operating System :: OS Independent
17
+ Classifier: Intended Audience :: Science/Research
18
+ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
19
+ Requires-Python: >=3.9
20
+ Description-Content-Type: text/markdown
21
+ License-File: LICENSE
22
+ Requires-Dist: duckdb>=1.0
23
+ Requires-Dist: pandas>=1.0
24
+ Requires-Dist: numpy>=1.20
25
+ Requires-Dist: matplotlib>=3.0
26
+ Requires-Dist: adjustText>=0.7
27
+ Provides-Extra: excel
28
+ Requires-Dist: openpyxl>=3.0; extra == "excel"
29
+ Dynamic: license-file
30
+
31
+ # de_quack
32
+
33
+ Python/R library for differential expression (DE) data management and visualization using DuckDB.
34
+
35
+ Stores DE analysis results with automatic gene annotation, enabling reproducible and efficient querying of experimental data.
36
+
37
+ ## Features
38
+
39
+ - **Efficient Storage**: DuckDB-backed persistence for gene expression results
40
+ - **Automatic Annotation**: Maps gene symbols and Ensembl IDs with canonical references
41
+ - **Flexible Querying**: Filter results using simple keyword arguments (e.g., `padj__lt=0.05`)
42
+ - **Multi-language Support**: Native Python and R interfaces
43
+ - **Visualization**: Built-in volcano plot generation with publication-ready styling
44
+ - **Data Normalization**: Handles variable column names and formats automatically
45
+
46
+ ## Installation
47
+
48
+ ```bash
49
+ pip install de_quack
50
+ ```
51
+
52
+ For Excel export support (optional):
53
+ ```bash
54
+ pip install de_quack[excel]
55
+ ```
56
+
57
+ ## Quick Start
58
+
59
+ ### Python
60
+
61
+ ```python
62
+ from de_quack import de_duckling, volcano_plot
63
+
64
+ with de_duckling('results.duckdb') as db:
65
+ db.initialize_gene_table('human')
66
+ db.insert_to_database('data.txt')
67
+ results = db.query('gene_results', padj__lt=0.05)
68
+ print(results)
69
+
70
+ # Generate volcano plot
71
+ volcano_plot(results, padj=0.05, log2fc=1, plot_file='volcano.png')
72
+ ```
73
+
74
+ ### R
75
+
76
+ ```r
77
+ # Find and source the wrapper directly from the pip installation directory
78
+ py_pkg_path <- dirname(reticulate::import("de_quack")$`__file__`)
79
+ source(file.path(py_pkg_path, "wrapper.R"))
80
+
81
+ # Initialize
82
+ duck <- de_quack(db_path = "results.duckdb")
83
+ duck$connect()
84
+ duck$initialize_gene_table('human')
85
+ duck$insert_to_database('data.txt')
86
+ results <- duck$query('gene_results', padj__lt=0.05)
87
+ duck$volcano_plot(results, padj=0.05, log2fc=1, plot_file='volcano.png')
88
+ duck$close()
89
+ ```
90
+
91
+ ## Database Schema
92
+
93
+ ### Tables
94
+
95
+ - **experimental_data**: Metadata about DE analysis experiments
96
+ - **gene_results**: Individual gene-level results with statistics
97
+ - **genes**: Reference gene annotations (human, etc.)
98
+
99
+ ### Advanced Querying & JSON Fallback
100
+ DeDuck supports intuitive field modifiers (`__lt`, `__gt`, `__lte`, `__gte`, `__ne`). If a metric isn't a native column in the database, DeDuck automatically queries it out of custom nested JSON metadata dynamically:
101
+
102
+ ```python
103
+ # Regular column filtering + automatic nested JSON key metadata extraction
104
+ with de_duckling as db:
105
+ results = db.query('gene_results', padj__lt=0.05, custom_biotype__ne='pseudogene')
106
+ ```
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+
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+ ## License
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+
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+ MIT
de_quack-0.1.0/src/de_quack.egg-info/SOURCES.txt ADDED
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+ LICENSE
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+ README.md
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+ pyproject.toml
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+ src/de_quack.egg-info/PKG-INFO
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+ src/de_quack.egg-info/SOURCES.txt
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+ src/de_quack.egg-info/dependency_links.txt
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+ src/de_quack.egg-info/requires.txt
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+ src/de_quack.egg-info/top_level.txt
de_quack-0.1.0/src/de_quack.egg-info/requires.txt ADDED
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+ duckdb>=1.0
2
+ pandas>=1.0
3
+ numpy>=1.20
4
+ matplotlib>=3.0
5
+ adjustText>=0.7
6
+
7
+ [excel]
8
+ openpyxl>=3.0