untangler 0.1.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- untangler-0.1.0.dist-info/METADATA +92 -0
- untangler-0.1.0.dist-info/RECORD +11 -0
- untangler-0.1.0.dist-info/WHEEL +5 -0
- untangler-0.1.0.dist-info/entry_points.txt +2 -0
- untangler-0.1.0.dist-info/licenses/LICENSE +674 -0
- untangler-0.1.0.dist-info/top_level.txt +2 -0
- untangler.py +98 -0
- untangler_modules/__init__.py +3 -0
- untangler_modules/cluster_transcripts.py +1483 -0
- untangler_modules/constants.py +21 -0
- untangler_modules/utils.py +104 -0
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Metadata-Version: 2.4
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Name: untangler
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Version: 0.1.0
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Summary: RNA-seq transcript-level analysis and clustering tool
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Author: Joshua Levendis
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License-Expression: GPL-3.0-only
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Project-URL: Homepage, https://github.com/levend1s/untangler
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Project-URL: Repository, https://github.com/levend1s/untangler
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Project-URL: Issues, https://github.com/levend1s/untangler/issues
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Keywords: RNA-seq,transcript analysis,BAM,bioinformatics
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Classifier: Development Status :: 2 - Pre-Alpha
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Classifier: Intended Audience :: Science/Research
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3 :: Only
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Classifier: Programming Language :: Python :: 3.9
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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: pandas
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Requires-Dist: numpy
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Requires-Dist: pysam
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Requires-Dist: scikit-learn
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Requires-Dist: scipy
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Requires-Dist: matplotlib
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Requires-Dist: statsmodels
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Requires-Dist: gffpandas
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Requires-Dist: igv-reports
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Dynamic: license-file
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# untangler
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Assembler for DNA, aligner for RNA against DNA, untangler for RNA subclusters
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## Install from PyPI
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```bash
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python -m pip install untangler
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```
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## Install from source
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```bash
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python -m pip install .
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```
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## Run from a source checkout
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```bash
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python3 -m venv .venv
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source .venv/bin/activate
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python -m pip install --upgrade pip
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python -m pip install -e .
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python untangler.py --help
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```
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The editable install uses the dependencies declared in `pyproject.toml` while
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running the code directly from the checkout. For example:
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```bash
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python untangler.py cluster_transcripts \
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--ids PF3D7_1007900 \
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-i config.txt \
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-o ./cluster_transcripts_PF3D7_1007900_28 \
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--cluster_cols introns,m6A \
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--predict introns \
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-t 0.6 -f --generate_igv_reports
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```
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For local development, install the editable package:
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```bash
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python -m pip install -e .
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```
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## Build and upload
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```bash
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python -m pip install build twine
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python -m build
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python -m twine upload dist/*
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```
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## Usage
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```bash
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untangler cluster_transcripts --ids PF3D7_1007900 \
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-i config.txt \
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-o ./cluster_transcripts_PF3D7_1007900_28 \
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--cluster_cols introns,m6A \
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--predict introns \
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-t 0.6 -f --generate_igv_reports
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```
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untangler.py,sha256=_2rt_QAPYE6eUCg5D82HS4WFyVaBRGClnT8ofJUpNXM,6372
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untangler-0.1.0.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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untangler_modules/__init__.py,sha256=kd79aLxktkGhL8Y9vS8QdeiwN7ynNIN1OBC8TSRMgR8,78
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untangler_modules/cluster_transcripts.py,sha256=ZBMVLcMNvFcWgNXSoElDLge4xM63fwfUvw-uyUS8xH4,59642
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untangler_modules/constants.py,sha256=XBYzqMvtODZzDJgVpupUadpoF5YTvySFvoHXqJfLEiM,519
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untangler_modules/utils.py,sha256=0XdBUN131ThfctCqaWvUypAp6zG_BdkwagTtTz-Qi40,3856
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untangler-0.1.0.dist-info/METADATA,sha256=u39X1_uQpet-cdRRZyS5P-gPJo8tVUhWWcza2eYYCEg,2253
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untangler-0.1.0.dist-info/WHEEL,sha256=YVMoNqKzERt-wjUZwJ33xBGAwnFl-4cqbYkTtWa4itE,91
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untangler-0.1.0.dist-info/entry_points.txt,sha256=37EP6uIqefh3EXF93loGIDagSt8fXDYPwmAiwWKFKcM,45
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untangler-0.1.0.dist-info/top_level.txt,sha256=EbKD21TTrvyEIgvWKmG31Bqy_yPOH-gHV-FsAac2CZc,28
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untangler-0.1.0.dist-info/RECORD,,
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