python-katlas 0.1.2__tar.gz → 0.1.3__tar.gz

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Files changed (23) hide show
  1. {python-katlas-0.1.2 → python_katlas-0.1.3}/LICENSE +0 -0
  2. {python-katlas-0.1.2 → python_katlas-0.1.3}/MANIFEST.in +0 -0
  3. {python-katlas-0.1.2/python_katlas.egg-info → python_katlas-0.1.3}/PKG-INFO +172 -65
  4. {python-katlas-0.1.2 → python_katlas-0.1.3}/README.md +152 -62
  5. python_katlas-0.1.3/katlas/__init__.py +1 -0
  6. {python-katlas-0.1.2 → python_katlas-0.1.3}/katlas/_modidx.py +2 -2
  7. {python-katlas-0.1.2 → python_katlas-0.1.3}/katlas/core.py +0 -0
  8. {python-katlas-0.1.2 → python_katlas-0.1.3}/katlas/dl.py +14 -14
  9. {python-katlas-0.1.2 → python_katlas-0.1.3}/katlas/feature.py +8 -5
  10. {python-katlas-0.1.2 → python_katlas-0.1.3}/katlas/imports.py +0 -0
  11. {python-katlas-0.1.2 → python_katlas-0.1.3}/katlas/plot.py +20 -20
  12. {python-katlas-0.1.2 → python_katlas-0.1.3}/katlas/train.py +7 -7
  13. {python-katlas-0.1.2 → python_katlas-0.1.3/python_katlas.egg-info}/PKG-INFO +172 -65
  14. {python-katlas-0.1.2 → python_katlas-0.1.3}/settings.ini +4 -3
  15. {python-katlas-0.1.2 → python_katlas-0.1.3}/setup.py +0 -0
  16. python-katlas-0.1.2/katlas/__init__.py +0 -1
  17. {python-katlas-0.1.2 → python_katlas-0.1.3}/python_katlas.egg-info/SOURCES.txt +0 -0
  18. {python-katlas-0.1.2 → python_katlas-0.1.3}/python_katlas.egg-info/dependency_links.txt +0 -0
  19. {python-katlas-0.1.2 → python_katlas-0.1.3}/python_katlas.egg-info/entry_points.txt +0 -0
  20. {python-katlas-0.1.2 → python_katlas-0.1.3}/python_katlas.egg-info/not-zip-safe +0 -0
  21. {python-katlas-0.1.2 → python_katlas-0.1.3}/python_katlas.egg-info/requires.txt +0 -0
  22. {python-katlas-0.1.2 → python_katlas-0.1.3}/python_katlas.egg-info/top_level.txt +0 -0
  23. {python-katlas-0.1.2 → python_katlas-0.1.3}/setup.cfg +0 -0
{python-katlas-0.1.2 → python_katlas-0.1.3}/LICENSE RENAMED
File without changes
{python-katlas-0.1.2 → python_katlas-0.1.3}/MANIFEST.in RENAMED
File without changes
{python-katlas-0.1.2/python_katlas.egg-info → python_katlas-0.1.3}/PKG-INFO RENAMED
@@ -1,8 +1,8 @@
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  Metadata-Version: 2.1
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  Name: python-katlas
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- Version: 0.1.2
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+ Version: 0.1.3
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  Summary: tools for predicting kinome specificities
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- Home-page: https://github.com/sky1ove/python-katlas
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+ Home-page: https://github.com/sky1ove/katlas
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  Author: lily
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  Author-email: lcai888666@gmail.com
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  License: Apache Software License 2.0
@@ -17,19 +17,37 @@ Classifier: Programming Language :: Python :: 3.10
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  Classifier: License :: OSI Approved :: Apache Software License
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  Requires-Python: >=3.7
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  Description-Content-Type: text/markdown
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- Provides-Extra: dev
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  License-File: LICENSE
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+ Requires-Dist: statsmodels
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+ Requires-Dist: fastparquet
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+ Requires-Dist: tqdm
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+ Provides-Extra: dev
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+ Requires-Dist: nbdev; extra == "dev"
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+ Requires-Dist: pyngrok; extra == "dev"
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+ Requires-Dist: fastai>=2.7.12; extra == "dev"
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+ Requires-Dist: fastbook; extra == "dev"
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+ Requires-Dist: fairscale; extra == "dev"
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+ Requires-Dist: fair-esm; extra == "dev"
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+ Requires-Dist: logomaker; extra == "dev"
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+ Requires-Dist: seaborn; extra == "dev"
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+ Requires-Dist: rdkit; extra == "dev"
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+ Requires-Dist: umap-learn; extra == "dev"
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+ Requires-Dist: adjustText; extra == "dev"
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+ Requires-Dist: bokeh; extra == "dev"
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+ Requires-Dist: scikit-learn>=1.3.0; extra == "dev"
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+ Requires-Dist: openpyxl; extra == "dev"
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  # KATLAS
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  <!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
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+ <img alt="Katlas logo" width="600" caption="Katlas logo" src="https://github.com/sky1ove/katlas/raw/main/dataset/images/logo.png" id="logo"/>
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+
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  <a target="_blank" href="https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/index.ipynb">
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  <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
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- </a>
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-
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- <img alt="Katlas logo" width="700" caption="Katlas logo" src="https://github.com/sky1ove/katlas/raw/main/dataset/images/logo.png" id="logo"/>
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+ </a> <a href="https://pypi.org/project/python-katlas/">
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+ <img src="https://img.shields.io/pypi/v/python-katlas?link=https%3A%2F%2Fpypi.org%2Fproject%2Fpython-katlas%2F" alt="PyPI"></a>
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  KATLAS is a repository containing python tools to predict kinases given
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  a substrate sequence. It also contains datasets of kinase substrate
@@ -38,9 +56,8 @@ specificities and human phosphoproteomics.
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  ***References***: Please cite the appropriate papers if KATLAS is
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  helpful to your research.
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- - KATLAS was described in the paper \[Decoding Human Kinome
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- Specificities through a Computational Data-Driven Approach
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- (manuscript)\]
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+ - KATLAS was described in the paper \[Computational Decoding of Human
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+ Kinome Substrate Specificities and Functions\]
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  - The positional scanning peptide array (PSPA) data is from paper [An
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  atlas of substrate specificities for the human serine/threonine
@@ -60,13 +77,21 @@ helpful to your research.
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  phosphoproteome](https://www.nature.com/articles/s41587-019-0344-3),
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  and [CPTAC](https://pdc.cancer.gov/pdc/cptac-pancancer) /
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  [LinkedOmics](https://academic.oup.com/nar/article/46/D1/D956/4607804)
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-
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-
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+
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+ ## Reproduce datasets & figures
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+
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+ Follow the instructions in katlas_raw:
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+ https://github.com/sky1ove/katlas_raw
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+
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+ Need to install the package via: `pip install 'python-katlas[dev]' -U`
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+
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  ## Web applications
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- Users can now run the analysis directly on the web without needing to code.
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+ Users can now run the analysis directly on the web without needing to
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+ code.
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- Check out our latest web: [kinase-atlas.com](https://kinase-atlas.com/)
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+ Check out our latest web platform:
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+ [kinase-atlas.com](https://kinase-atlas.com/)
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  ## Tutorials on Colab
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@@ -77,14 +102,12 @@ Check out our latest web: [kinase-atlas.com](https://kinase-atlas.com/)
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  - 3. [Kinase enrichment analysis for AKT
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  inhibitor](https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/tutorial_03a_enrichment_AKTi.ipynb)
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-
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  ## Install
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83
- Install the latest version through pip
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+ pip install python-katlas -U
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85
- ``` python
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- pip install python-katlas -Uq
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- ```
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+ To use other modules besides the core, do
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+ `pip install 'python-katlas[dev]' -U`
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  ## Import
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@@ -217,7 +240,18 @@ get_pct('AEEKEyHSEGG',**param_PSPA_y, pct_ref = y_pct)
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  considering string: ['-5A', '-4E', '-3E', '-2K', '-1E', '0Y', '1H', '2S', '3E', '4G', '5G']
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-
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+ <div>
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+ <style scoped>
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+ .dataframe tbody tr th:only-of-type {
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+ vertical-align: middle;
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+ }
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+ &#10; .dataframe tbody tr th {
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+ vertical-align: top;
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+ }
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+ &#10; .dataframe thead th {
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+ text-align: right;
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+ }
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+ </style>
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  | | log2(score) | percentile |
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  |-------|-------------|------------|
@@ -233,7 +267,8 @@ get_pct('AEEKEyHSEGG',**param_PSPA_y, pct_ref = y_pct)
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  | TNK2 | -4.577 | 2.050581 |
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  | DDR2 | -4.920 | 10.403281 |
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-
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+ <p>93 rows × 2 columns</p>
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+ </div>
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  ## High-throughput substrate scoring on a dataframe
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@@ -251,6 +286,18 @@ df = Data.get_ochoa_site().head()
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  df.iloc[:,-2:]
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  ```
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+ <div>
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+ <style scoped>
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+ .dataframe tbody tr th:only-of-type {
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+ vertical-align: middle;
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+ }
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+ &#10; .dataframe tbody tr th {
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+ vertical-align: top;
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+ }
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+ &#10; .dataframe thead th {
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+ text-align: right;
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+ }
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+ </style>
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  | | site_seq | gene_site |
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  |-----|-----------------|----------------|
@@ -260,7 +307,7 @@ df.iloc[:,-2:]
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  | 3 | KSRFTEYSMTSSVMR | A0A075B6Q4_S68 |
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  | 4 | FTEYSMTSSVMRRNE | A0A075B6Q4_S71 |
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+ </div>
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  ### Set the column name and param to calculate
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@@ -279,17 +326,29 @@ results
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  100%|██████████| 289/289 [00:05<00:00, 56.64it/s]
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-
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- | kinase | SRC | EPHA3 | FES | NTRK3 | ALK | EPHA8 | ABL1 | FLT3 | EPHB2 | FYN | ... | MEK5 | PKN2 | MAP2K7 | MRCKB | HIPK3 | CDK8 | BUB1 | MEKK3 | MAP2K3 | GRK1 |
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- |--------|----------|----------|----------|----------|----------|----------|----------|----------|----------|----------|-----|----------|----------|----------|----------|----------|----------|----------|----------|----------|----------|
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- | 0 | 0.991760 | 1.093712 | 1.051750 | 1.067134 | 1.013682 | 1.097519 | 0.966379 | 0.982464 | 1.054986 | 1.055910 | ... | 1.314859 | 1.635470 | 1.652251 | 1.622672 | 1.362973 | 1.797155 | 1.305198 | 1.423618 | 1.504941 | 1.872020 |
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- | 1 | 0.910262 | 0.953743 | 0.942327 | 0.950601 | 0.872694 | 0.932586 | 0.846899 | 0.826662 | 0.915020 | 0.942713 | ... | 1.175454 | 1.402006 | 1.430392 | 1.215826 | 1.569373 | 1.716455 | 1.270999 | 1.195081 | 1.223082 | 1.793290 |
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- | 2 | 0.849866 | 0.899910 | 0.848895 | 0.879652 | 0.874959 | 0.899414 | 0.839200 | 0.836523 | 0.858040 | 0.867269 | ... | 1.408003 | 1.813739 | 1.454786 | 1.084522 | 1.352556 | 1.524663 | 1.377839 | 1.173830 | 1.305691 | 1.811849 |
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- | 3 | 0.803826 | 0.836527 | 0.800759 | 0.894570 | 0.839905 | 0.781001 | 0.847847 | 0.807040 | 0.805877 | 0.801402 | ... | 1.110307 | 1.703637 | 1.795092 | 1.469653 | 1.549936 | 1.491344 | 1.446922 | 1.055452 | 1.534895 | 1.741090 |
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- | 4 | 0.822793 | 0.796532 | 0.792343 | 0.839882 | 0.810122 | 0.781420 | 0.805251 | 0.795022 | 0.790380 | 0.864538 | ... | 1.062617 | 1.357689 | 1.485945 | 1.249266 | 1.456078 | 1.422782 | 1.376471 | 1.089629 | 1.121309 | 1.697524 |
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-
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+ <div>
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+ <style scoped>
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+ .dataframe tbody tr th:only-of-type {
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+ vertical-align: middle;
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+ }
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+ &#10; .dataframe tbody tr th {
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+ vertical-align: top;
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+ }
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+ &#10; .dataframe thead th {
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+ text-align: right;
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+ }
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+ </style>
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+
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+ | kinase | SRC | EPHA3 | FES | NTRK3 | ALK | EPHA8 | ABL1 | FLT3 | EPHB2 | FYN | ... | MEK5 | PKN2 | MAP2K7 | MRCKB | HIPK3 | CDK8 | BUB1 | MEKK3 | MAP2K3 | GRK1 |
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+ |----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
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+ | 0 | 0.991760 | 1.093712 | 1.051750 | 1.067134 | 1.013682 | 1.097519 | 0.966379 | 0.982464 | 1.054986 | 1.055910 | ... | 1.314859 | 1.635470 | 1.652251 | 1.622672 | 1.362973 | 1.797155 | 1.305198 | 1.423618 | 1.504941 | 1.872020 |
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+ | 1 | 0.910262 | 0.953743 | 0.942327 | 0.950601 | 0.872694 | 0.932586 | 0.846899 | 0.826662 | 0.915020 | 0.942713 | ... | 1.175454 | 1.402006 | 1.430392 | 1.215826 | 1.569373 | 1.716455 | 1.270999 | 1.195081 | 1.223082 | 1.793290 |
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+ | 2 | 0.849866 | 0.899910 | 0.848895 | 0.879652 | 0.874959 | 0.899414 | 0.839200 | 0.836523 | 0.858040 | 0.867269 | ... | 1.408003 | 1.813739 | 1.454786 | 1.084522 | 1.352556 | 1.524663 | 1.377839 | 1.173830 | 1.305691 | 1.811849 |
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+ | 3 | 0.803826 | 0.836527 | 0.800759 | 0.894570 | 0.839905 | 0.781001 | 0.847847 | 0.807040 | 0.805877 | 0.801402 | ... | 1.110307 | 1.703637 | 1.795092 | 1.469653 | 1.549936 | 1.491344 | 1.446922 | 1.055452 | 1.534895 | 1.741090 |
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+ | 4 | 0.822793 | 0.796532 | 0.792343 | 0.839882 | 0.810122 | 0.781420 | 0.805251 | 0.795022 | 0.790380 | 0.864538 | ... | 1.062617 | 1.357689 | 1.485945 | 1.249266 | 1.456078 | 1.422782 | 1.376471 | 1.089629 | 1.121309 | 1.697524 |
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+ <p>5 rows × 289 columns</p>
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+ </div>
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  ## Phosphorylation sites
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@@ -303,15 +362,26 @@ df = Data.get_cptac_ensembl_site()
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  df.head(3)
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  ```
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- | | gene | site | site_seq | protein | gene_name | gene_site | protein_site |
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- |-----|--------------------|-------|-----------------|-------------------|-----------|-------------|-----------------------|
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- | 0 | ENSG00000003056.8 | S267 | DDQLGEESEERDDHL | ENSP00000000412.3 | M6PR | M6PR_S267 | ENSP00000000412_S267 |
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- | 1 | ENSG00000003056.8 | S267 | DDQLGEESEERDDHL | ENSP00000440488.2 | M6PR | M6PR_S267 | ENSP00000440488_S267 |
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- | 2 | ENSG00000048028.11 | S1053 | PPTIRPNSPYDLCSR | ENSP00000003302.4 | USP28 | USP28_S1053 | ENSP00000003302_S1053 |
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+ | | gene | site | site_seq | protein | gene_name | gene_site | protein_site |
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+ |----|----|----|----|----|----|----|----|
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+ | 0 | ENSG00000003056.8 | S267 | DDQLGEESEERDDHL | ENSP00000000412.3 | M6PR | M6PR_S267 | ENSP00000000412_S267 |
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+ | 1 | ENSG00000003056.8 | S267 | DDQLGEESEERDDHL | ENSP00000440488.2 | M6PR | M6PR_S267 | ENSP00000440488_S267 |
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+ | 2 | ENSG00000048028.11 | S1053 | PPTIRPNSPYDLCSR | ENSP00000003302.4 | USP28 | USP28_S1053 | ENSP00000003302_S1053 |
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+ </div>
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  ### [Ochoa et al. human phosphoproteome](https://www.nature.com/articles/s41587-019-0344-3)
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@@ -320,14 +390,26 @@ df = Data.get_ochoa_site()
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  ```
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- | | uniprot | position | residue | is_disopred | disopred_score | log10_hotspot_pval_min | isHotspot | uniprot_position | functional_score | current_uniprot | name | gene | Sequence | is_valid | site_seq | gene_site |
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- |-----|------------|----------|---------|-------------|----------------|------------------------|-----------|------------------|------------------|-----------------|------------------|------|---------------------------------------------------|----------|-----------------|----------------|
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- | 0 | A0A075B6Q4 | 24 | S | True | 0.91 | 6.839384 | True | A0A075B6Q4_24 | 0.149257 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | VDDEKGDSNDDYDSA | A0A075B6Q4_S24 |
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- | 1 | A0A075B6Q4 | 35 | S | True | 0.87 | 9.192622 | False | A0A075B6Q4_35 | 0.136966 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | YDSAGLLSDEDCMSV | A0A075B6Q4_S35 |
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- | 2 | A0A075B6Q4 | 57 | S | False | 0.28 | 0.818834 | False | A0A075B6Q4_57 | 0.125364 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | IADHLFWSEETKSRF | A0A075B6Q4_S57 |
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+ <style scoped>
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+ .dataframe tbody tr th:only-of-type {
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+ vertical-align: middle;
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+ }
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+ &#10; .dataframe tbody tr th {
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+ vertical-align: top;
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+ }
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+ &#10; .dataframe thead th {
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+ | | uniprot | position | residue | is_disopred | disopred_score | log10_hotspot_pval_min | isHotspot | uniprot_position | functional_score | current_uniprot | name | gene | Sequence | is_valid | site_seq | gene_site |
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+ |----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
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+ | 0 | A0A075B6Q4 | 24 | S | True | 0.91 | 6.839384 | True | A0A075B6Q4_24 | 0.149257 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | VDDEKGDSNDDYDSA | A0A075B6Q4_S24 |
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+ | 1 | A0A075B6Q4 | 35 | S | True | 0.87 | 9.192622 | False | A0A075B6Q4_35 | 0.136966 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | YDSAGLLSDEDCMSV | A0A075B6Q4_S35 |
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+ | 2 | A0A075B6Q4 | 57 | S | False | 0.28 | 0.818834 | False | A0A075B6Q4_57 | 0.125364 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | IADHLFWSEETKSRF | A0A075B6Q4_S57 |
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  ### PhosphoSitePlus human phosphorylation site
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@@ -336,14 +418,26 @@ df = Data.get_psp_human_site()
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  ```
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- | | gene | protein | uniprot | site | gene_site | SITE_GRP_ID | species | site_seq | LT_LIT | MS_LIT | MS_CST | CST_CAT# | Ambiguous_Site |
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- |-----|-------|-------------|---------|------|-----------|-------------|---------|-----------------------|--------|--------|--------|----------|----------------|
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- | 0 | YWHAB | 14-3-3 beta | P31946 | T2 | YWHAB_T2 | 15718712 | human | \_\_\_\_\_\_MtMDksELV | NaN | 3.0 | 1.0 | None | 0 |
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- | 1 | YWHAB | 14-3-3 beta | P31946 | S6 | YWHAB_S6 | 15718709 | human | \_\_MtMDksELVQkAk | NaN | 8.0 | NaN | None | 0 |
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- | 2 | YWHAB | 14-3-3 beta | P31946 | Y21 | YWHAB_Y21 | 3426383 | human | LAEQAERyDDMAAAM | NaN | NaN | 4.0 | None | 0 |
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+ }
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+ &#10; .dataframe tbody tr th {
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+ vertical-align: top;
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+ }
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+ &#10; .dataframe thead th {
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+ text-align: right;
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+ }
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+ </style>
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+
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+ | | gene | protein | uniprot | site | gene_site | SITE_GRP_ID | species | site_seq | LT_LIT | MS_LIT | MS_CST | CST_CAT# | Ambiguous_Site |
435
+ |----|----|----|----|----|----|----|----|----|----|----|----|----|----|
436
+ | 0 | YWHAB | 14-3-3 beta | P31946 | T2 | YWHAB_T2 | 15718712 | human | \_\_\_\_\_\_MtMDksELV | NaN | 3.0 | 1.0 | None | 0 |
437
+ | 1 | YWHAB | 14-3-3 beta | P31946 | S6 | YWHAB_S6 | 15718709 | human | \_\_MtMDksELVQkAk | NaN | 8.0 | NaN | None | 0 |
438
+ | 2 | YWHAB | 14-3-3 beta | P31946 | Y21 | YWHAB_Y21 | 3426383 | human | LAEQAERyDDMAAAM | NaN | NaN | 4.0 | None | 0 |
439
+
440
+ </div>
347
441
 
348
442
  ### Unique sites of combined Ochoa & PhosphoSitePlus
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443
 
@@ -352,14 +446,27 @@ df = Data.get_combine_site_psp_ochoa()
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446
  df.head(3)
353
447
  ```
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448
 
355
-
356
- | | site_seq | gene_site | gene | source | num_site | acceptor | -7 | -6 | -5 | -4 | ... | -2 | -1 | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
357
- |-----|-----------------|------------|-------|--------|----------|----------|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
358
- | 0 | AAAAAAASGGAGSDN | PBX1_S136 | PBX1 | ochoa | 1 | S | A | A | A | A | ... | A | A | S | G | G | A | G | S | D | N |
359
- | 1 | AAAAAAASGGGVSPD | PBX2_S146 | PBX2 | ochoa | 1 | S | A | A | A | A | ... | A | A | S | G | G | G | V | S | P | D |
360
- | 2 | AAAAAAASGVTTGKP | CLASR_S349 | CLASR | ochoa | 1 | S | A | A | A | A | ... | A | A | S | G | V | T | T | G | K | P |
361
-
362
-
449
+ <div>
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+ <style scoped>
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+ .dataframe tbody tr th:only-of-type {
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+ vertical-align: middle;
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+ }
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+ &#10; .dataframe tbody tr th {
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+ vertical-align: top;
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+ }
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+ &#10; .dataframe thead th {
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+ text-align: right;
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+ }
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+ </style>
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+
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+ | | site_seq | gene_site | gene | source | num_site | acceptor | -7 | -6 | -5 | -4 | ... | -2 | -1 | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
463
+ |----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
464
+ | 0 | AAAAAAASGGAGSDN | PBX1_S136 | PBX1 | ochoa | 1 | S | A | A | A | A | ... | A | A | S | G | G | A | G | S | D | N |
465
+ | 1 | AAAAAAASGGGVSPD | PBX2_S146 | PBX2 | ochoa | 1 | S | A | A | A | A | ... | A | A | S | G | G | G | V | S | P | D |
466
+ | 2 | AAAAAAASGVTTGKP | CLASR_S349 | CLASR | ochoa | 1 | S | A | A | A | A | ... | A | A | S | G | V | T | T | G | K | P |
467
+
468
+ <p>3 rows × 21 columns</p>
469
+ </div>
363
470
 
364
471
  ## Phosphorylation site sequence example
365
472