PyPI - python-katlas - Versions diffs - 0.1.2__tar.gz → 0.1.4__tar.gz - Mend

python-katlas 0.1.2tar.gz → 0.1.4tar.gz

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{python-katlas-0.1.2 → python_katlas-0.1.4}/LICENSE RENAMED Viewed

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{python-katlas-0.1.2 → python_katlas-0.1.4}/MANIFEST.in RENAMED Viewed

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{python-katlas-0.1.2/python_katlas.egg-info → python_katlas-0.1.4}/PKG-INFO RENAMED Viewed

@@ -1,8 +1,8 @@
 Metadata-Version: 2.1
 Name: python-katlas
-Version: 0.1.2
+Version: 0.1.4
 Summary: tools for predicting kinome specificities
-Home-page: https://github.com/sky1ove/python-katlas
+Home-page: https://github.com/sky1ove/katlas
 Author: lily
 Author-email: lcai888666@gmail.com
 License: Apache Software License 2.0
@@ -17,19 +17,35 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: License :: OSI Approved :: Apache Software License
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
-Provides-Extra: dev
 License-File: LICENSE
+Requires-Dist: statsmodels
+Requires-Dist: fastparquet
+Requires-Dist: tqdm
+Provides-Extra: dev
+Requires-Dist: nbdev; extra == "dev"
+Requires-Dist: pyngrok; extra == "dev"
+Requires-Dist: fastai>=2.7.12; extra == "dev"
+Requires-Dist: fastbook; extra == "dev"
+Requires-Dist: fairscale; extra == "dev"
+Requires-Dist: fair-esm; extra == "dev"
+Requires-Dist: logomaker; extra == "dev"
+Requires-Dist: seaborn; extra == "dev"
+Requires-Dist: rdkit; extra == "dev"
+Requires-Dist: umap-learn; extra == "dev"
+Requires-Dist: adjustText; extra == "dev"
+Requires-Dist: bokeh; extra == "dev"
+Requires-Dist: scikit-learn>=1.3.0; extra == "dev"
+Requires-Dist: openpyxl; extra == "dev"
 # KATLAS
 <!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
-<a target="_blank" href="https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/index.ipynb">
-<img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
-</a>
+<img alt="Katlas logo" width="600" caption="Katlas logo" src="https://github.com/sky1ove/katlas/raw/main/dataset/images/logo.png" id="logo"/>
-<img alt="Katlas logo" width="700" caption="Katlas logo" src="https://github.com/sky1ove/katlas/raw/main/dataset/images/logo.png" id="logo"/>
+<p><a target="_blank" href="https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/index.ipynb"><img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/></a>
+<a href="https://pypi.org/project/python-katlas/"><img src="https://img.shields.io/pypi/v/python-katlas?link=https%3A%2F%2Fpypi.org%2Fproject%2Fpython-katlas%2F" alt="PyPI"></a></p>
 KATLAS is a repository containing python tools to predict kinases given
 a substrate sequence. It also contains datasets of kinase substrate
@@ -38,9 +54,8 @@ specificities and human phosphoproteomics.
 ***References***: Please cite the appropriate papers if KATLAS is
 helpful to your research.
-- KATLAS was described in the paper \[Decoding Human Kinome
-  Specificities through a Computational Data-Driven Approach
-  (manuscript)\]
+- KATLAS was described in the paper \[Computational Decoding of Human
+  Kinome Substrate Specificities and Functions\]
 - The positional scanning peptide array (PSPA) data is from paper [An
   atlas of substrate specificities for the human serine/threonine
@@ -60,13 +75,21 @@ helpful to your research.
   phosphoproteome](https://www.nature.com/articles/s41587-019-0344-3),
   and [CPTAC](https://pdc.cancer.gov/pdc/cptac-pancancer) /
   [LinkedOmics](https://academic.oup.com/nar/article/46/D1/D956/4607804)
+## Reproduce datasets & figures
+Follow the instructions in katlas_raw:
+https://github.com/sky1ove/katlas_raw
+Need to install the package via: `pip install 'python-katlas[dev]' -U`
 ## Web applications
-Users can now run the analysis directly on the web without needing to code.
+Users can now run the analysis directly on the web without needing to
+code.
-Check out our latest web: [kinase-atlas.com](https://kinase-atlas.com/)
+Check out our latest web platform:
+[kinase-atlas.com](https://kinase-atlas.com/)
 ## Tutorials on Colab
@@ -77,14 +100,12 @@ Check out our latest web: [kinase-atlas.com](https://kinase-atlas.com/)
 - 3.  [Kinase enrichment analysis for AKT
       inhibitor](https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/tutorial_03a_enrichment_AKTi.ipynb)
 ## Install
-Install the latest version through pip
+    pip install python-katlas -U
-``` python
-pip install python-katlas -Uq
-```
+To use other modules besides the core, do
+`pip install 'python-katlas[dev]' -U`
 ## Import
@@ -233,6 +254,7 @@ get_pct('AEEKEyHSEGG',**param_PSPA_y, pct_ref = y_pct)
 | TNK2  | -4.577      | 2.050581   |
 | DDR2  | -4.920      | 10.403281  |
+<p>93 rows × 2 columns</p>
 ## High-throughput substrate scoring on a dataframe
@@ -252,6 +274,7 @@ df.iloc[:,-2:]
 ```
 |     | site_seq        | gene_site      |
 |-----|-----------------|----------------|
 | 0   | VDDEKGDSNDDYDSA | A0A075B6Q4_S24 |
@@ -281,14 +304,15 @@ results
-| kinase | SRC      | EPHA3    | FES      | NTRK3    | ALK      | EPHA8    | ABL1     | FLT3     | EPHB2    | FYN      | ... | MEK5     | PKN2     | MAP2K7   | MRCKB    | HIPK3    | CDK8     | BUB1     | MEKK3    | MAP2K3   | GRK1     |
-|--------|----------|----------|----------|----------|----------|----------|----------|----------|----------|----------|-----|----------|----------|----------|----------|----------|----------|----------|----------|----------|----------|
-| 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 |
-| 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 |
-| 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 |
-| 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 |
-| 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 |
+| kinase | SRC | EPHA3 | FES | NTRK3 | ALK | EPHA8 | ABL1 | FLT3 | EPHB2 | FYN | ... | MEK5 | PKN2 | MAP2K7 | MRCKB | HIPK3 | CDK8 | BUB1 | MEKK3 | MAP2K3 | GRK1 |
+|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
+| 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 |
+| 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 |
+| 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 |
+| 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 |
+| 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 |
+<p>5 rows × 289 columns</p>
 ## Phosphorylation sites
@@ -305,11 +329,11 @@ df.head(3)
-|     | gene               | site  | site_seq        | protein           | gene_name | gene_site   | protein_site          |
-|-----|--------------------|-------|-----------------|-------------------|-----------|-------------|-----------------------|
-| 0   | ENSG00000003056.8  | S267  | DDQLGEESEERDDHL | ENSP00000000412.3 | M6PR      | M6PR_S267   | ENSP00000000412_S267  |
-| 1   | ENSG00000003056.8  | S267  | DDQLGEESEERDDHL | ENSP00000440488.2 | M6PR      | M6PR_S267   | ENSP00000440488_S267  |
-| 2   | ENSG00000048028.11 | S1053 | PPTIRPNSPYDLCSR | ENSP00000003302.4 | USP28     | USP28_S1053 | ENSP00000003302_S1053 |
+|  | gene | site | site_seq | protein | gene_name | gene_site | protein_site |
+|----|----|----|----|----|----|----|----|
+| 0 | ENSG00000003056.8 | S267 | DDQLGEESEERDDHL | ENSP00000000412.3 | M6PR | M6PR_S267 | ENSP00000000412_S267 |
+| 1 | ENSG00000003056.8 | S267 | DDQLGEESEERDDHL | ENSP00000440488.2 | M6PR | M6PR_S267 | ENSP00000440488_S267 |
+| 2 | ENSG00000048028.11 | S1053 | PPTIRPNSPYDLCSR | ENSP00000003302.4 | USP28 | USP28_S1053 | ENSP00000003302_S1053 |
@@ -321,11 +345,12 @@ df.head(3)
 ```
-|     | 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      |
-|-----|------------|----------|---------|-------------|----------------|------------------------|-----------|------------------|------------------|-----------------|------------------|------|---------------------------------------------------|----------|-----------------|----------------|
-| 0   | A0A075B6Q4 | 24       | S       | True        | 0.91           | 6.839384               | True      | A0A075B6Q4_24    | 0.149257         | A0A075B6Q4      | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True     | VDDEKGDSNDDYDSA | A0A075B6Q4_S24 |
-| 1   | A0A075B6Q4 | 35       | S       | True        | 0.87           | 9.192622               | False     | A0A075B6Q4_35    | 0.136966         | A0A075B6Q4      | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True     | YDSAGLLSDEDCMSV | A0A075B6Q4_S35 |
-| 2   | A0A075B6Q4 | 57       | S       | False       | 0.28           | 0.818834               | False     | A0A075B6Q4_57    | 0.125364         | A0A075B6Q4      | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True     | IADHLFWSEETKSRF | A0A075B6Q4_S57 |
+|  | 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 |
+|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
+| 0 | A0A075B6Q4 | 24 | S | True | 0.91 | 6.839384 | True | A0A075B6Q4_24 | 0.149257 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | VDDEKGDSNDDYDSA | A0A075B6Q4_S24 |
+| 1 | A0A075B6Q4 | 35 | S | True | 0.87 | 9.192622 | False | A0A075B6Q4_35 | 0.136966 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | YDSAGLLSDEDCMSV | A0A075B6Q4_S35 |
+| 2 | A0A075B6Q4 | 57 | S | False | 0.28 | 0.818834 | False | A0A075B6Q4_57 | 0.125364 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | IADHLFWSEETKSRF | A0A075B6Q4_S57 |
@@ -337,11 +362,12 @@ df.head(3)
 ```
-|     | gene  | protein     | uniprot | site | gene_site | SITE_GRP_ID | species | site_seq              | LT_LIT | MS_LIT | MS_CST | CST_CAT# | Ambiguous_Site |
-|-----|-------|-------------|---------|------|-----------|-------------|---------|-----------------------|--------|--------|--------|----------|----------------|
-| 0   | YWHAB | 14-3-3 beta | P31946  | T2   | YWHAB_T2  | 15718712    | human   | \_\_\_\_\_\_MtMDksELV | NaN    | 3.0    | 1.0    | None     | 0              |
-| 1   | YWHAB | 14-3-3 beta | P31946  | S6   | YWHAB_S6  | 15718709    | human   | \_\_MtMDksELVQkAk     | NaN    | 8.0    | NaN    | None     | 0              |
-| 2   | YWHAB | 14-3-3 beta | P31946  | Y21  | YWHAB_Y21 | 3426383     | human   | LAEQAERyDDMAAAM       | NaN    | NaN    | 4.0    | None     | 0              |
+|  | gene | protein | uniprot | site | gene_site | SITE_GRP_ID | species | site_seq | LT_LIT | MS_LIT | MS_CST | CST_CAT# | Ambiguous_Site |
+|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
+| 0 | YWHAB | 14-3-3 beta | P31946 | T2 | YWHAB_T2 | 15718712 | human | \_\_\_\_\_\_MtMDksELV | NaN | 3.0 | 1.0 | None | 0 |
+| 1 | YWHAB | 14-3-3 beta | P31946 | S6 | YWHAB_S6 | 15718709 | human | \_\_MtMDksELVQkAk | NaN | 8.0 | NaN | None | 0 |
+| 2 | YWHAB | 14-3-3 beta | P31946 | Y21 | YWHAB_Y21 | 3426383 | human | LAEQAERyDDMAAAM | NaN | NaN | 4.0 | None | 0 |
@@ -353,12 +379,14 @@ df.head(3)
 ```
-|     | site_seq        | gene_site  | gene  | source | num_site | acceptor | -7  | -6  | -5  | -4  | ... | -2  | -1  | 0   | 1   | 2   | 3   | 4   | 5   | 6   | 7   |
-|-----|-----------------|------------|-------|--------|----------|----------|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
-| 0   | AAAAAAASGGAGSDN | PBX1_S136  | PBX1  | ochoa  | 1        | S        | A   | A   | A   | A   | ... | A   | A   | S   | G   | G   | A   | G   | S   | D   | N   |
-| 1   | AAAAAAASGGGVSPD | PBX2_S146  | PBX2  | ochoa  | 1        | S        | A   | A   | A   | A   | ... | A   | A   | S   | G   | G   | G   | V   | S   | P   | D   |
-| 2   | AAAAAAASGVTTGKP | CLASR_S349 | CLASR | ochoa  | 1        | S        | A   | A   | A   | A   | ... | A   | A   | S   | G   | V   | T   | T   | G   | K   | P   |
+|  | site_seq | gene_site | gene | source | num_site | acceptor | -7 | -6 | -5 | -4 | ... | -2 | -1 | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
+|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
+| 0 | AAAAAAASGGAGSDN | PBX1_S136 | PBX1 | ochoa | 1 | S | A | A | A | A | ... | A | A | S | G | G | A | G | S | D | N |
+| 1 | AAAAAAASGGGVSPD | PBX2_S146 | PBX2 | ochoa | 1 | S | A | A | A | A | ... | A | A | S | G | G | G | V | S | P | D |
+| 2 | AAAAAAASGVTTGKP | CLASR_S349 | CLASR | ochoa | 1 | S | A | A | A | A | ... | A | A | S | G | V | T | T | G | K | P |
+<p>3 rows × 21 columns</p>
 ## Phosphorylation site sequence example

{python-katlas-0.1.2 → python_katlas-0.1.4}/README.md RENAMED Viewed

@@ -3,11 +3,10 @@
 <!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
-<a target="_blank" href="https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/index.ipynb">
-<img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
-</a>
+<img alt="Katlas logo" width="600" caption="Katlas logo" src="https://github.com/sky1ove/katlas/raw/main/dataset/images/logo.png" id="logo"/>
-<img alt="Katlas logo" width="700" caption="Katlas logo" src="https://github.com/sky1ove/katlas/raw/main/dataset/images/logo.png" id="logo"/>
+<p><a target="_blank" href="https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/index.ipynb"><img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/></a>
+<a href="https://pypi.org/project/python-katlas/"><img src="https://img.shields.io/pypi/v/python-katlas?link=https%3A%2F%2Fpypi.org%2Fproject%2Fpython-katlas%2F" alt="PyPI"></a></p>
 KATLAS is a repository containing python tools to predict kinases given
 a substrate sequence. It also contains datasets of kinase substrate
@@ -16,9 +15,8 @@ specificities and human phosphoproteomics.
 ***References***: Please cite the appropriate papers if KATLAS is
 helpful to your research.
-- KATLAS was described in the paper \[Decoding Human Kinome
-  Specificities through a Computational Data-Driven Approach
-  (manuscript)\]
+- KATLAS was described in the paper \[Computational Decoding of Human
+  Kinome Substrate Specificities and Functions\]
 - The positional scanning peptide array (PSPA) data is from paper [An
   atlas of substrate specificities for the human serine/threonine
@@ -38,13 +36,21 @@ helpful to your research.
   phosphoproteome](https://www.nature.com/articles/s41587-019-0344-3),
   and [CPTAC](https://pdc.cancer.gov/pdc/cptac-pancancer) /
   [LinkedOmics](https://academic.oup.com/nar/article/46/D1/D956/4607804)
+## Reproduce datasets & figures
+Follow the instructions in katlas_raw:
+https://github.com/sky1ove/katlas_raw
+Need to install the package via: `pip install 'python-katlas[dev]' -U`
 ## Web applications
-Users can now run the analysis directly on the web without needing to code.
+Users can now run the analysis directly on the web without needing to
+code.
-Check out our latest web: [kinase-atlas.com](https://kinase-atlas.com/)
+Check out our latest web platform:
+[kinase-atlas.com](https://kinase-atlas.com/)
 ## Tutorials on Colab
@@ -55,14 +61,12 @@ Check out our latest web: [kinase-atlas.com](https://kinase-atlas.com/)
 - 3.  [Kinase enrichment analysis for AKT
       inhibitor](https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/tutorial_03a_enrichment_AKTi.ipynb)
 ## Install
-Install the latest version through pip
+    pip install python-katlas -U
-``` python
-pip install python-katlas -Uq
-```
+To use other modules besides the core, do
+`pip install 'python-katlas[dev]' -U`
 ## Import
@@ -211,6 +215,7 @@ get_pct('AEEKEyHSEGG',**param_PSPA_y, pct_ref = y_pct)
 | TNK2  | -4.577      | 2.050581   |
 | DDR2  | -4.920      | 10.403281  |
+<p>93 rows × 2 columns</p>
 ## High-throughput substrate scoring on a dataframe
@@ -230,6 +235,7 @@ df.iloc[:,-2:]
 ```
 |     | site_seq        | gene_site      |
 |-----|-----------------|----------------|
 | 0   | VDDEKGDSNDDYDSA | A0A075B6Q4_S24 |
@@ -259,14 +265,15 @@ results
-| kinase | SRC      | EPHA3    | FES      | NTRK3    | ALK      | EPHA8    | ABL1     | FLT3     | EPHB2    | FYN      | ... | MEK5     | PKN2     | MAP2K7   | MRCKB    | HIPK3    | CDK8     | BUB1     | MEKK3    | MAP2K3   | GRK1     |
-|--------|----------|----------|----------|----------|----------|----------|----------|----------|----------|----------|-----|----------|----------|----------|----------|----------|----------|----------|----------|----------|----------|
-| 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 |
-| 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 |
-| 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 |
-| 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 |
-| 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 |
+| kinase | SRC | EPHA3 | FES | NTRK3 | ALK | EPHA8 | ABL1 | FLT3 | EPHB2 | FYN | ... | MEK5 | PKN2 | MAP2K7 | MRCKB | HIPK3 | CDK8 | BUB1 | MEKK3 | MAP2K3 | GRK1 |
+|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
+| 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 |
+| 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 |
+| 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 |
+| 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 |
+| 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 |
+<p>5 rows × 289 columns</p>
 ## Phosphorylation sites
@@ -283,11 +290,11 @@ df.head(3)
-|     | gene               | site  | site_seq        | protein           | gene_name | gene_site   | protein_site          |
-|-----|--------------------|-------|-----------------|-------------------|-----------|-------------|-----------------------|
-| 0   | ENSG00000003056.8  | S267  | DDQLGEESEERDDHL | ENSP00000000412.3 | M6PR      | M6PR_S267   | ENSP00000000412_S267  |
-| 1   | ENSG00000003056.8  | S267  | DDQLGEESEERDDHL | ENSP00000440488.2 | M6PR      | M6PR_S267   | ENSP00000440488_S267  |
-| 2   | ENSG00000048028.11 | S1053 | PPTIRPNSPYDLCSR | ENSP00000003302.4 | USP28     | USP28_S1053 | ENSP00000003302_S1053 |
+|  | gene | site | site_seq | protein | gene_name | gene_site | protein_site |
+|----|----|----|----|----|----|----|----|
+| 0 | ENSG00000003056.8 | S267 | DDQLGEESEERDDHL | ENSP00000000412.3 | M6PR | M6PR_S267 | ENSP00000000412_S267 |
+| 1 | ENSG00000003056.8 | S267 | DDQLGEESEERDDHL | ENSP00000440488.2 | M6PR | M6PR_S267 | ENSP00000440488_S267 |
+| 2 | ENSG00000048028.11 | S1053 | PPTIRPNSPYDLCSR | ENSP00000003302.4 | USP28 | USP28_S1053 | ENSP00000003302_S1053 |
@@ -299,11 +306,12 @@ df.head(3)
 ```
-|     | 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      |
-|-----|------------|----------|---------|-------------|----------------|------------------------|-----------|------------------|------------------|-----------------|------------------|------|---------------------------------------------------|----------|-----------------|----------------|
-| 0   | A0A075B6Q4 | 24       | S       | True        | 0.91           | 6.839384               | True      | A0A075B6Q4_24    | 0.149257         | A0A075B6Q4      | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True     | VDDEKGDSNDDYDSA | A0A075B6Q4_S24 |
-| 1   | A0A075B6Q4 | 35       | S       | True        | 0.87           | 9.192622               | False     | A0A075B6Q4_35    | 0.136966         | A0A075B6Q4      | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True     | YDSAGLLSDEDCMSV | A0A075B6Q4_S35 |
-| 2   | A0A075B6Q4 | 57       | S       | False       | 0.28           | 0.818834               | False     | A0A075B6Q4_57    | 0.125364         | A0A075B6Q4      | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True     | IADHLFWSEETKSRF | A0A075B6Q4_S57 |
+|  | 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 |
+|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
+| 0 | A0A075B6Q4 | 24 | S | True | 0.91 | 6.839384 | True | A0A075B6Q4_24 | 0.149257 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | VDDEKGDSNDDYDSA | A0A075B6Q4_S24 |
+| 1 | A0A075B6Q4 | 35 | S | True | 0.87 | 9.192622 | False | A0A075B6Q4_35 | 0.136966 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | YDSAGLLSDEDCMSV | A0A075B6Q4_S35 |
+| 2 | A0A075B6Q4 | 57 | S | False | 0.28 | 0.818834 | False | A0A075B6Q4_57 | 0.125364 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | IADHLFWSEETKSRF | A0A075B6Q4_S57 |
@@ -315,11 +323,12 @@ df.head(3)
 ```
-|     | gene  | protein     | uniprot | site | gene_site | SITE_GRP_ID | species | site_seq              | LT_LIT | MS_LIT | MS_CST | CST_CAT# | Ambiguous_Site |
-|-----|-------|-------------|---------|------|-----------|-------------|---------|-----------------------|--------|--------|--------|----------|----------------|
-| 0   | YWHAB | 14-3-3 beta | P31946  | T2   | YWHAB_T2  | 15718712    | human   | \_\_\_\_\_\_MtMDksELV | NaN    | 3.0    | 1.0    | None     | 0              |
-| 1   | YWHAB | 14-3-3 beta | P31946  | S6   | YWHAB_S6  | 15718709    | human   | \_\_MtMDksELVQkAk     | NaN    | 8.0    | NaN    | None     | 0              |
-| 2   | YWHAB | 14-3-3 beta | P31946  | Y21  | YWHAB_Y21 | 3426383     | human   | LAEQAERyDDMAAAM       | NaN    | NaN    | 4.0    | None     | 0              |
+|  | gene | protein | uniprot | site | gene_site | SITE_GRP_ID | species | site_seq | LT_LIT | MS_LIT | MS_CST | CST_CAT# | Ambiguous_Site |
+|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
+| 0 | YWHAB | 14-3-3 beta | P31946 | T2 | YWHAB_T2 | 15718712 | human | \_\_\_\_\_\_MtMDksELV | NaN | 3.0 | 1.0 | None | 0 |
+| 1 | YWHAB | 14-3-3 beta | P31946 | S6 | YWHAB_S6 | 15718709 | human | \_\_MtMDksELVQkAk | NaN | 8.0 | NaN | None | 0 |
+| 2 | YWHAB | 14-3-3 beta | P31946 | Y21 | YWHAB_Y21 | 3426383 | human | LAEQAERyDDMAAAM | NaN | NaN | 4.0 | None | 0 |
@@ -331,12 +340,14 @@ df.head(3)
 ```
-|     | site_seq        | gene_site  | gene  | source | num_site | acceptor | -7  | -6  | -5  | -4  | ... | -2  | -1  | 0   | 1   | 2   | 3   | 4   | 5   | 6   | 7   |
-|-----|-----------------|------------|-------|--------|----------|----------|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
-| 0   | AAAAAAASGGAGSDN | PBX1_S136  | PBX1  | ochoa  | 1        | S        | A   | A   | A   | A   | ... | A   | A   | S   | G   | G   | A   | G   | S   | D   | N   |
-| 1   | AAAAAAASGGGVSPD | PBX2_S146  | PBX2  | ochoa  | 1        | S        | A   | A   | A   | A   | ... | A   | A   | S   | G   | G   | G   | V   | S   | P   | D   |
-| 2   | AAAAAAASGVTTGKP | CLASR_S349 | CLASR | ochoa  | 1        | S        | A   | A   | A   | A   | ... | A   | A   | S   | G   | V   | T   | T   | G   | K   | P   |
+|  | site_seq | gene_site | gene | source | num_site | acceptor | -7 | -6 | -5 | -4 | ... | -2 | -1 | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
+|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
+| 0 | AAAAAAASGGAGSDN | PBX1_S136 | PBX1 | ochoa | 1 | S | A | A | A | A | ... | A | A | S | G | G | A | G | S | D | N |
+| 1 | AAAAAAASGGGVSPD | PBX2_S146 | PBX2 | ochoa | 1 | S | A | A | A | A | ... | A | A | S | G | G | G | V | S | P | D |
+| 2 | AAAAAAASGVTTGKP | CLASR_S349 | CLASR | ochoa | 1 | S | A | A | A | A | ... | A | A | S | G | V | T | T | G | K | P |
+<p>3 rows × 21 columns</p>
 ## Phosphorylation site sequence example

python_katlas-0.1.4/katlas/__init__.py ADDED Viewed

	@@ -0,0 +1 @@
1	+ __version__ = "0.1.4"

{python-katlas-0.1.2 → python_katlas-0.1.4}/katlas/_modidx.py RENAMED Viewed

@@ -1,9 +1,9 @@
 # Autogenerated by nbdev
 d = { 'settings': { 'branch': 'main',
-                'doc_baseurl': '/python-katlas',
+                'doc_baseurl': '/katlas',
                 'doc_host': 'https://sky1ove.github.io',
-                'git_url': 'https://github.com/sky1ove/python-katlas',
+                'git_url': 'https://github.com/sky1ove/katlas',
                 'lib_path': 'katlas'},
   'syms': { 'katlas.core': { 'katlas.core.CPTAC': ('core.html#cptac', 'katlas/core.py'),
                              'katlas.core.CPTAC._fetch_data': ('core.html#cptac._fetch_data', 'katlas/core.py'),

{python-katlas-0.1.2 → python_katlas-0.1.4}/katlas/core.py RENAMED Viewed

File without changes

{python-katlas-0.1.2 → python_katlas-0.1.4}/katlas/dl.py RENAMED Viewed

@@ -6,7 +6,7 @@
 __all__ = ['def_device', 'seed_everything', 'GeneralDataset', 'get_sampler', 'MLP_1', 'CNN1D_1', 'init_weights', 'lin_wn',
            'conv_wn', 'CNN1D_2', 'train_dl', 'train_dl_cv', 'predict_dl']
-# %% ../nbs/04_DL.ipynb 5
+# %% ../nbs/04_DL.ipynb 4
 from fastbook import *
 import fastcore.all as fc,torch.nn.init as init
 from fastai.callback.training import GradientClip
@@ -22,7 +22,7 @@ from sklearn.model_selection import *
 from sklearn.metrics import mean_squared_error
 from scipy.stats import spearmanr,pearsonr
-# %% ../nbs/04_DL.ipynb 7
+# %% ../nbs/04_DL.ipynb 6
 def seed_everything(seed=123):
     random.seed(seed)
     os.environ['PYTHONHASHSEED'] = str(seed)
@@ -32,10 +32,10 @@ def seed_everything(seed=123):
     torch.backends.cudnn.deterministic = True
     torch.backends.cudnn.benchmark = False
-# %% ../nbs/04_DL.ipynb 9
+# %% ../nbs/04_DL.ipynb 8
 def_device = 'mps' if torch.backends.mps.is_available() else 'cuda' if torch.cuda.is_available() else 'cpu'
-# %% ../nbs/04_DL.ipynb 14
+# %% ../nbs/04_DL.ipynb 13
 class GeneralDataset:
     def __init__(self,
                  df, # a dataframe of values
@@ -62,7 +62,7 @@ class GeneralDataset:
             y = torch.Tensor(self.y[index])
             return X, y
-# %% ../nbs/04_DL.ipynb 18
+# %% ../nbs/04_DL.ipynb 17
 def get_sampler(info,col):
     "For imbalanced data, get higher weights for less-represented samples"
@@ -82,7 +82,7 @@ def get_sampler(info,col):
     return sampler
-# %% ../nbs/04_DL.ipynb 24
+# %% ../nbs/04_DL.ipynb 23
 def MLP_1(num_features,
           num_targets,
           hidden_units = [512, 218],
@@ -112,7 +112,7 @@ def MLP_1(num_features,
     return model
-# %% ../nbs/04_DL.ipynb 30
+# %% ../nbs/04_DL.ipynb 29
 class CNN1D_1(Module):
     def __init__(self,
@@ -137,12 +137,12 @@ class CNN1D_1(Module):
         x = self.fc2(x)
         return x
-# %% ../nbs/04_DL.ipynb 34
+# %% ../nbs/04_DL.ipynb 33
 def init_weights(m, leaky=0.):
     "Initiate any Conv layer with Kaiming norm."
     if isinstance(m, (nn.Conv1d,nn.Conv2d,nn.Conv3d)): init.kaiming_normal_(m.weight, a=leaky)
-# %% ../nbs/04_DL.ipynb 35
+# %% ../nbs/04_DL.ipynb 34
 def lin_wn(ni,nf,dp=0.1,act=nn.SiLU):
     "Weight norm of linear."
     layers =  nn.Sequential(
@@ -152,7 +152,7 @@ def lin_wn(ni,nf,dp=0.1,act=nn.SiLU):
     if act: layers.append(act())
     return layers
-# %% ../nbs/04_DL.ipynb 36
+# %% ../nbs/04_DL.ipynb 35
 def conv_wn(ni, nf, ks=3, stride=1, padding=1, dp=0.1,act=nn.ReLU):
     "Weight norm of conv."
     layers =  nn.Sequential(
@@ -162,7 +162,7 @@ def conv_wn(ni, nf, ks=3, stride=1, padding=1, dp=0.1,act=nn.ReLU):
     if act: layers.append(act())
     return layers
-# %% ../nbs/04_DL.ipynb 37
+# %% ../nbs/04_DL.ipynb 36
 class CNN1D_2(nn.Module):
     def __init__(self, ni, nf, amp_scale = 16):
@@ -212,7 +212,7 @@ class CNN1D_2(nn.Module):
         return x
-# %% ../nbs/04_DL.ipynb 41
+# %% ../nbs/04_DL.ipynb 40
 def train_dl(df,
             feat_col,
             target_col,
@@ -275,7 +275,7 @@ def train_dl(df,
     return target, pred
-# %% ../nbs/04_DL.ipynb 46
+# %% ../nbs/04_DL.ipynb 45
 @fc.delegates(train_dl)
 def train_dl_cv(df,
                 feat_col,
@@ -325,7 +325,7 @@ def train_dl_cv(df,
     return oof, metrics
-# %% ../nbs/04_DL.ipynb 54
+# %% ../nbs/04_DL.ipynb 53
 def predict_dl(df,
                feat_col,
                target_col,

{python-katlas-0.1.2 → python_katlas-0.1.4}/katlas/feature.py RENAMED Viewed

@@ -5,7 +5,7 @@
 # %% auto 0
 __all__ = ['get_rdkit', 'get_morgan', 'get_esm', 'get_t5', 'get_t5_bfd', 'reduce_feature', 'remove_hi_corr', 'preprocess']
-# %% ../nbs/01_feature.ipynb 5
+# %% ../nbs/01_feature.ipynb 4
 from fastbook import *
 import torch,re,joblib,gc,esm
 from tqdm.notebook import tqdm; tqdm.pandas()
@@ -14,7 +14,7 @@ from .core import Data
 # Rdkit
 from rdkit import Chem
 from rdkit.ML.Descriptors import MoleculeDescriptors
-from rdkit.Chem import Draw,Descriptors,AllChem
+from rdkit.Chem import Draw,Descriptors,AllChem,rdFingerprintGenerator
 # Models
 from fairscale.nn.data_parallel import FullyShardedDataParallel as FSDP
@@ -30,7 +30,7 @@ from umap.umap_ import UMAP
 set_config(transform_output="pandas")
-# %% ../nbs/01_feature.ipynb 8
+# %% ../nbs/01_feature.ipynb 7
 def get_rdkit(df: pd.DataFrame, # a dataframe that contains smiles
               col:str = "SMILES", # colname of smile
               normalize: bool = True, # normalize features using StandardScaler()
@@ -49,14 +49,17 @@ def get_rdkit(df: pd.DataFrame, # a dataframe that contains smiles
     # feature_df = feature_df.reset_index()
     return feature_df
-# %% ../nbs/01_feature.ipynb 12
+# %% ../nbs/01_feature.ipynb 11
 def get_morgan(df: pd.DataFrame, # a dataframe that contains smiles
                col: str = "SMILES", # colname of smile
                radius=3
               ):
     "Get 2048 morgan fingerprint (binary feature) from smiles in a dataframe"
     mols = [Chem.MolFromSmiles(smi) for smi in df[col]]
-    morgan_fps = [AllChem.GetMorganFingerprintAsBitVect(mol, radius=radius, nBits=2048) for mol in mols]
+    mfpgen = rdFingerprintGenerator.GetMorganGenerator(radius=radius,fpSize=2048)
+    morgan_fps = [mfpgen.GetFingerprint(mol) for mol in mols]
     fp_df = pd.DataFrame(np.array(morgan_fps), index=df.index)
     fp_df.columns = "morgan_" + fp_df.columns.astype(str)
     return fp_df

{python-katlas-0.1.2 → python_katlas-0.1.4}/katlas/imports.py RENAMED Viewed

File without changes

{python-katlas-0.1.2 → python_katlas-0.1.4}/katlas/plot.py RENAMED Viewed

@@ -7,7 +7,7 @@ __all__ = ['set_sns', 'get_color_dict', 'logo_func', 'get_logo', 'get_logo2', 'p
            'plot_cluster', 'plot_bokeh', 'plot_count', 'plot_bar', 'plot_group_bar', 'plot_box', 'plot_corr',
            'draw_corr', 'get_AUCDF', 'plot_confusion_matrix']
-# %% ../nbs/02_plot.ipynb 5
+# %% ../nbs/02_plot.ipynb 4
 import joblib,logomaker
 import fastcore.all as fc, pandas as pd, numpy as np, seaborn as sns
 from adjustText import adjust_text
@@ -32,14 +32,14 @@ from bokeh.layouts import column
 from bokeh.palettes import Category20_20
 from itertools import cycle
-# %% ../nbs/02_plot.ipynb 7
+# %% ../nbs/02_plot.ipynb 6
 def set_sns():
     "Set seaborn resolution for notebook display"
     sns.set(rc={"figure.dpi":300, 'savefig.dpi':300})
     sns.set_context('notebook')
     sns.set_style("ticks")
-# %% ../nbs/02_plot.ipynb 8
+# %% ../nbs/02_plot.ipynb 7
 def get_color_dict(categories, # list of names to assign color
                    palette: str='tab20', # choose from sns.color_palette
                    ):
@@ -49,7 +49,7 @@ def get_color_dict(categories, # list of names to assign color
     color_map = {category: next(color_cycle) for category in categories}
     return color_map
-# %% ../nbs/02_plot.ipynb 12
+# %% ../nbs/02_plot.ipynb 11
 def logo_func(df:pd.DataFrame, # a dataframe that contains ratios for each amino acid at each position
               title: str='logo', # title of the motif logo
              ):
@@ -81,7 +81,7 @@ def logo_func(df:pd.DataFrame, # a dataframe that contains ratios for each amino
     logo.ax.set_yticks([])
     logo.ax.set_title(title)
-# %% ../nbs/02_plot.ipynb 13
+# %% ../nbs/02_plot.ipynb 12
 def get_logo(df: pd.DataFrame, # stacked Dataframe with kinase as index, substrates as columns
              kinase: str, # a specific kinase name in index
              ):
@@ -120,7 +120,7 @@ def get_logo(df: pd.DataFrame, # stacked Dataframe with kinase as index, substra
     # plot logo
     logo_func(ratio2, kinase)
-# %% ../nbs/02_plot.ipynb 17
+# %% ../nbs/02_plot.ipynb 16
 def get_logo2(full: pd.DataFrame, # a dataframe that contains the full matrix of a kinase, with index as amino acid, and columns as positions
               title: str = 'logo', # title of the graph
               ):
@@ -159,7 +159,7 @@ def get_logo2(full: pd.DataFrame, # a dataframe that contains the full matrix of
     logo_func(ratio2,title)
-# %% ../nbs/02_plot.ipynb 20
+# %% ../nbs/02_plot.ipynb 19
 @fc.delegates(sns.scatterplot)
 def plot_rank(sorted_df: pd.DataFrame, # a sorted dataframe
               x: str, # column name for x axis
@@ -203,7 +203,7 @@ def plot_rank(sorted_df: pd.DataFrame, # a sorted dataframe
     plt.tight_layout()
-# %% ../nbs/02_plot.ipynb 24
+# %% ../nbs/02_plot.ipynb 23
 @fc.delegates(sns.histplot)
 def plot_hist(df: pd.DataFrame, # a dataframe that contain values for plot
               x: str, # column name of values
@@ -220,7 +220,7 @@ def plot_hist(df: pd.DataFrame, # a dataframe that contain values for plot
     plt.figure(figsize=figsize)
     sns.histplot(data=df,x=x,**hist_params,**kwargs)
-# %% ../nbs/02_plot.ipynb 28
+# %% ../nbs/02_plot.ipynb 27
 @fc.delegates(sns.heatmap)
 def plot_heatmap(matrix, # a matrix of values
                  title: str='heatmap', # title of the heatmap
@@ -235,7 +235,7 @@ def plot_heatmap(matrix, # a matrix of values
     sns.heatmap(matrix, cmap=cmap, annot=False,**kwargs)
     plt.title(title)
-# %% ../nbs/02_plot.ipynb 32
+# %% ../nbs/02_plot.ipynb 31
 @fc.delegates(sns.scatterplot)
 def plot_2d(X: pd.DataFrame, # a dataframe that has first column to be x, and second column to be y
             **kwargs, # arguments for sns.scatterplot
@@ -244,7 +244,7 @@ def plot_2d(X: pd.DataFrame, # a dataframe that has first column to be x, and se
     plt.figure(figsize=(7,7))
     sns.scatterplot(data = X,x=X.columns[0],y=X.columns[1],alpha=0.7,**kwargs)
-# %% ../nbs/02_plot.ipynb 34
+# %% ../nbs/02_plot.ipynb 33
 def plot_cluster(df: pd.DataFrame, # a dataframe of values that is waited for dimensionality reduction
                  method: str='pca', # dimensionality reduction method, choose from pca, umap, and tsne
                  hue: str=None, # colname of color
@@ -266,10 +266,10 @@ def plot_cluster(df: pd.DataFrame, # a dataframe of values that is waited for di
     plt.xticks([])
     plt.yticks([])
     if name_list is not None:
-        texts = [plt.text(embedding_df[x_col][i], embedding_df[y_col][i], name_list[i],fontsize=8) for i in range(len(embedding_df))]
+        texts = [plt.text(embedding_df[x_col].iloc[i], embedding_df[y_col].iloc[i], name_list[i],fontsize=8) for i in range(len(embedding_df))]
         adjust_text(texts, arrowprops=dict(arrowstyle='-', color='black'))
-# %% ../nbs/02_plot.ipynb 38
+# %% ../nbs/02_plot.ipynb 37
 def plot_bokeh(X:pd.DataFrame, # a dataframe of two columns from dimensionality reduction
                idx, # pd.Series or list that indicates identities for searching box
                hue:None, # pd.Series or list that indicates category for each sample
@@ -367,7 +367,7 @@ def plot_bokeh(X:pd.DataFrame, # a dataframe of two columns from dimensionality
     layout = column(autocomplete, p)
     show(layout)
-# %% ../nbs/02_plot.ipynb 41
+# %% ../nbs/02_plot.ipynb 40
 def plot_count(cnt, # from df['x'].value_counts()
                tick_spacing: float= None, # tick spacing for x axis
                palette: str='tab20'):
@@ -383,7 +383,7 @@ def plot_count(cnt, # from df['x'].value_counts()
     if tick_spacing is not None:
         ax.xaxis.set_major_locator(MultipleLocator(tick_spacing))
-# %% ../nbs/02_plot.ipynb 43
+# %% ../nbs/02_plot.ipynb 42
 @fc.delegates(sns.barplot)
 def plot_bar(df,
              value, # colname of value
@@ -403,7 +403,7 @@ def plot_bar(df,
     idx = df.groupby(group)[value].mean().sort_values(ascending=ascending).index
-    sns.barplot(data=df, x=group, y=value, order=idx, **kwargs)
+    sns.barplot(data=df, x=group, y=value, order=idx,hue=group, legend=False, **kwargs)
     if dots:
         marker = {'marker': 'o',
@@ -438,7 +438,7 @@ def plot_bar(df,
     plt.gca().spines[['right', 'top']].set_visible(False)
-# %% ../nbs/02_plot.ipynb 46
+# %% ../nbs/02_plot.ipynb 45
 @fc.delegates(sns.barplot)
 def plot_group_bar(df,
                    value_cols,  # list of column names for values, the order depends on the first item
@@ -459,8 +459,13 @@ def plot_group_bar(df,
     plt.figure(figsize=figsize)
     # Create the bar plot
-    sns.barplot(data=df_melted, x=group, y='Value', hue='Ranking', order=order,
-                capsize=0.1,errwidth=1.5,errcolor='gray', # adjust the error bar settings
+    sns.barplot(data=df_melted,
+                x=group,
+                y='Value',
+                hue='Ranking',
+                order=order,
+                capsize=0.1,
+                err_kws={'linewidth': 1.5,'color': 'gray'},
                 **kwargs)
     # Increase font size for the x-axis and y-axis tick labels
@@ -481,7 +486,7 @@ def plot_group_bar(df,
     plt.gca().spines[['right', 'top']].set_visible(False)
     plt.legend(fontsize=fontsize) # if change legend location, use loc='upper right'
-# %% ../nbs/02_plot.ipynb 49
+# %% ../nbs/02_plot.ipynb 48
 @fc.delegates(sns.boxplot)
 def plot_box(df,
              value, # colname of value
@@ -501,7 +506,7 @@ def plot_box(df,
     idx = df[[group,value]].groupby(group).median().sort_values(value,ascending=False).index
-    sns.boxplot(data=df, x=group, y=value, order=idx, **kwargs)
+    sns.boxplot(data=df, x=group, y=value, order=idx,hue=group, legend=False, **kwargs)
     if dots:
         sns.stripplot(x=group, y=value, data=df, order=idx, jitter=True, color='black', size=3)
@@ -523,7 +528,7 @@ def plot_box(df,
     # plt.gca().spines[['right', 'top']].set_visible(False)
-# %% ../nbs/02_plot.ipynb 52
+# %% ../nbs/02_plot.ipynb 51
 @fc.delegates(sns.regplot)
 def plot_corr(x, # x axis values, or colname of x axis
               y, # y axis values, or colname of y axis
@@ -560,7 +565,7 @@ def plot_corr(x, # x axis values, or colname of x axis
             transform=plt.gca().transAxes,
              ha='center', va='center')
-# %% ../nbs/02_plot.ipynb 56
+# %% ../nbs/02_plot.ipynb 55
 def draw_corr(corr):
     "plot heatmap from df.corr()"
@@ -572,7 +577,7 @@ def draw_corr(corr):
     plt.figure(figsize=(20, 16))  # Set the figure size
     sns.heatmap(corr, annot=True, cmap='coolwarm', vmin=-1, vmax=1, mask=mask, fmt='.2f')
-# %% ../nbs/02_plot.ipynb 60
+# %% ../nbs/02_plot.ipynb 59
 def get_AUCDF(df,col, reverse=False,plot=True,xlabel='Rank of reported kinase'):
     "Plot CDF curve and get relative area under the curve"
@@ -637,7 +642,7 @@ def get_AUCDF(df,col, reverse=False,plot=True,xlabel='Rank of reported kinase'):
     return AUCDF
-# %% ../nbs/02_plot.ipynb 63
+# %% ../nbs/02_plot.ipynb 62
 def plot_confusion_matrix(target, # pd.Series
                           pred, # pd.Series
                           class_names:list=['0','1'],

{python-katlas-0.1.2 → python_katlas-0.1.4}/katlas/train.py RENAMED Viewed

@@ -5,7 +5,7 @@
 # %% auto 0
 __all__ = ['get_splits', 'split_data', 'score_each', 'train_ml', 'train_ml_cv', 'predict_ml']
-# %% ../nbs/03_ML.ipynb 5
+# %% ../nbs/03_ML.ipynb 4
 # katlas
 from .core import Data
 from .feature import *
@@ -29,7 +29,7 @@ from sklearn.ensemble import *
 from sklearn import set_config
 set_config(transform_output="pandas")
-# %% ../nbs/03_ML.ipynb 8
+# %% ../nbs/03_ML.ipynb 7
 def get_splits(df: pd.DataFrame, # df contains info for split
                stratified: str=None, # colname to make stratified kfold; sampling from different groups
                group: str=None, # colname to make group kfold; test and train are from different groups
@@ -79,7 +79,7 @@ def get_splits(df: pd.DataFrame, # df contains info for split
     return splits
-# %% ../nbs/03_ML.ipynb 13
+# %% ../nbs/03_ML.ipynb 12
 def split_data(df: pd.DataFrame, # dataframe of values
                feat_col: list, # feature columns
                target_col: list, # target columns
@@ -95,7 +95,7 @@ def split_data(df: pd.DataFrame, # dataframe of values
     return X_train, y_train, X_test, y_test
-# %% ../nbs/03_ML.ipynb 17
+# %% ../nbs/03_ML.ipynb 16
 def score_each(target: pd.DataFrame, # target dataframe
               pred: pd.DataFrame, # predicted dataframe
               absolute = True, # if absolute, take average with absolute values for pearson/spearman
@@ -134,7 +134,7 @@ def score_each(target: pd.DataFrame, # target dataframe
     return mse,pearson_mean, metrics_df
-# %% ../nbs/03_ML.ipynb 22
+# %% ../nbs/03_ML.ipynb 21
 def train_ml(df, # dataframe of values
              feat_col, # feature columns
              target_col, # target columns
@@ -169,7 +169,7 @@ def train_ml(df, # dataframe of values
     return y_test, y_pred
-# %% ../nbs/03_ML.ipynb 25
+# %% ../nbs/03_ML.ipynb 24
 def train_ml_cv( df, # dataframe of values
                  feat_col, # feature columns
                  target_col,  # target columns
@@ -213,7 +213,7 @@ def train_ml_cv( df, # dataframe of values
     return oof, metrics
-# %% ../nbs/03_ML.ipynb 32
+# %% ../nbs/03_ML.ipynb 31
 def predict_ml(df, # Dataframe that contains features
                feat_col, # feature columns
                target_col=None,

{python-katlas-0.1.2 → python_katlas-0.1.4/python_katlas.egg-info}/PKG-INFO RENAMED Viewed

@@ -1,8 +1,8 @@
 Metadata-Version: 2.1
 Name: python-katlas
-Version: 0.1.2
+Version: 0.1.4
 Summary: tools for predicting kinome specificities
-Home-page: https://github.com/sky1ove/python-katlas
+Home-page: https://github.com/sky1ove/katlas
 Author: lily
 Author-email: lcai888666@gmail.com
 License: Apache Software License 2.0
@@ -17,19 +17,35 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: License :: OSI Approved :: Apache Software License
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
-Provides-Extra: dev
 License-File: LICENSE
+Requires-Dist: statsmodels
+Requires-Dist: fastparquet
+Requires-Dist: tqdm
+Provides-Extra: dev
+Requires-Dist: nbdev; extra == "dev"
+Requires-Dist: pyngrok; extra == "dev"
+Requires-Dist: fastai>=2.7.12; extra == "dev"
+Requires-Dist: fastbook; extra == "dev"
+Requires-Dist: fairscale; extra == "dev"
+Requires-Dist: fair-esm; extra == "dev"
+Requires-Dist: logomaker; extra == "dev"
+Requires-Dist: seaborn; extra == "dev"
+Requires-Dist: rdkit; extra == "dev"
+Requires-Dist: umap-learn; extra == "dev"
+Requires-Dist: adjustText; extra == "dev"
+Requires-Dist: bokeh; extra == "dev"
+Requires-Dist: scikit-learn>=1.3.0; extra == "dev"
+Requires-Dist: openpyxl; extra == "dev"
 # KATLAS
 <!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
-<a target="_blank" href="https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/index.ipynb">
-<img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
-</a>
+<img alt="Katlas logo" width="600" caption="Katlas logo" src="https://github.com/sky1ove/katlas/raw/main/dataset/images/logo.png" id="logo"/>
-<img alt="Katlas logo" width="700" caption="Katlas logo" src="https://github.com/sky1ove/katlas/raw/main/dataset/images/logo.png" id="logo"/>
+<p><a target="_blank" href="https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/index.ipynb"><img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/></a>
+<a href="https://pypi.org/project/python-katlas/"><img src="https://img.shields.io/pypi/v/python-katlas?link=https%3A%2F%2Fpypi.org%2Fproject%2Fpython-katlas%2F" alt="PyPI"></a></p>
 KATLAS is a repository containing python tools to predict kinases given
 a substrate sequence. It also contains datasets of kinase substrate
@@ -38,9 +54,8 @@ specificities and human phosphoproteomics.
 ***References***: Please cite the appropriate papers if KATLAS is
 helpful to your research.
-- KATLAS was described in the paper \[Decoding Human Kinome
-  Specificities through a Computational Data-Driven Approach
-  (manuscript)\]
+- KATLAS was described in the paper \[Computational Decoding of Human
+  Kinome Substrate Specificities and Functions\]
 - The positional scanning peptide array (PSPA) data is from paper [An
   atlas of substrate specificities for the human serine/threonine
@@ -60,13 +75,21 @@ helpful to your research.
   phosphoproteome](https://www.nature.com/articles/s41587-019-0344-3),
   and [CPTAC](https://pdc.cancer.gov/pdc/cptac-pancancer) /
   [LinkedOmics](https://academic.oup.com/nar/article/46/D1/D956/4607804)
+## Reproduce datasets & figures
+Follow the instructions in katlas_raw:
+https://github.com/sky1ove/katlas_raw
+Need to install the package via: `pip install 'python-katlas[dev]' -U`
 ## Web applications
-Users can now run the analysis directly on the web without needing to code.
+Users can now run the analysis directly on the web without needing to
+code.
-Check out our latest web: [kinase-atlas.com](https://kinase-atlas.com/)
+Check out our latest web platform:
+[kinase-atlas.com](https://kinase-atlas.com/)
 ## Tutorials on Colab
@@ -77,14 +100,12 @@ Check out our latest web: [kinase-atlas.com](https://kinase-atlas.com/)
 - 3.  [Kinase enrichment analysis for AKT
       inhibitor](https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/tutorial_03a_enrichment_AKTi.ipynb)
 ## Install
-Install the latest version through pip
+    pip install python-katlas -U
-``` python
-pip install python-katlas -Uq
-```
+To use other modules besides the core, do
+`pip install 'python-katlas[dev]' -U`
 ## Import
@@ -233,6 +254,7 @@ get_pct('AEEKEyHSEGG',**param_PSPA_y, pct_ref = y_pct)
 | TNK2  | -4.577      | 2.050581   |
 | DDR2  | -4.920      | 10.403281  |
+<p>93 rows × 2 columns</p>
 ## High-throughput substrate scoring on a dataframe
@@ -252,6 +274,7 @@ df.iloc[:,-2:]
 ```
 |     | site_seq        | gene_site      |
 |-----|-----------------|----------------|
 | 0   | VDDEKGDSNDDYDSA | A0A075B6Q4_S24 |
@@ -281,14 +304,15 @@ results
-| kinase | SRC      | EPHA3    | FES      | NTRK3    | ALK      | EPHA8    | ABL1     | FLT3     | EPHB2    | FYN      | ... | MEK5     | PKN2     | MAP2K7   | MRCKB    | HIPK3    | CDK8     | BUB1     | MEKK3    | MAP2K3   | GRK1     |
-|--------|----------|----------|----------|----------|----------|----------|----------|----------|----------|----------|-----|----------|----------|----------|----------|----------|----------|----------|----------|----------|----------|
-| 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 |
-| 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 |
-| 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 |
-| 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 |
-| 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 |
+| kinase | SRC | EPHA3 | FES | NTRK3 | ALK | EPHA8 | ABL1 | FLT3 | EPHB2 | FYN | ... | MEK5 | PKN2 | MAP2K7 | MRCKB | HIPK3 | CDK8 | BUB1 | MEKK3 | MAP2K3 | GRK1 |
+|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
+| 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 |
+| 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 |
+| 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 |
+| 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 |
+| 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 |
+<p>5 rows × 289 columns</p>
 ## Phosphorylation sites
@@ -305,11 +329,11 @@ df.head(3)
-|     | gene               | site  | site_seq        | protein           | gene_name | gene_site   | protein_site          |
-|-----|--------------------|-------|-----------------|-------------------|-----------|-------------|-----------------------|
-| 0   | ENSG00000003056.8  | S267  | DDQLGEESEERDDHL | ENSP00000000412.3 | M6PR      | M6PR_S267   | ENSP00000000412_S267  |
-| 1   | ENSG00000003056.8  | S267  | DDQLGEESEERDDHL | ENSP00000440488.2 | M6PR      | M6PR_S267   | ENSP00000440488_S267  |
-| 2   | ENSG00000048028.11 | S1053 | PPTIRPNSPYDLCSR | ENSP00000003302.4 | USP28     | USP28_S1053 | ENSP00000003302_S1053 |
+|  | gene | site | site_seq | protein | gene_name | gene_site | protein_site |
+|----|----|----|----|----|----|----|----|
+| 0 | ENSG00000003056.8 | S267 | DDQLGEESEERDDHL | ENSP00000000412.3 | M6PR | M6PR_S267 | ENSP00000000412_S267 |
+| 1 | ENSG00000003056.8 | S267 | DDQLGEESEERDDHL | ENSP00000440488.2 | M6PR | M6PR_S267 | ENSP00000440488_S267 |
+| 2 | ENSG00000048028.11 | S1053 | PPTIRPNSPYDLCSR | ENSP00000003302.4 | USP28 | USP28_S1053 | ENSP00000003302_S1053 |
@@ -321,11 +345,12 @@ df.head(3)
 ```
-|     | 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      |
-|-----|------------|----------|---------|-------------|----------------|------------------------|-----------|------------------|------------------|-----------------|------------------|------|---------------------------------------------------|----------|-----------------|----------------|
-| 0   | A0A075B6Q4 | 24       | S       | True        | 0.91           | 6.839384               | True      | A0A075B6Q4_24    | 0.149257         | A0A075B6Q4      | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True     | VDDEKGDSNDDYDSA | A0A075B6Q4_S24 |
-| 1   | A0A075B6Q4 | 35       | S       | True        | 0.87           | 9.192622               | False     | A0A075B6Q4_35    | 0.136966         | A0A075B6Q4      | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True     | YDSAGLLSDEDCMSV | A0A075B6Q4_S35 |
-| 2   | A0A075B6Q4 | 57       | S       | False       | 0.28           | 0.818834               | False     | A0A075B6Q4_57    | 0.125364         | A0A075B6Q4      | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True     | IADHLFWSEETKSRF | A0A075B6Q4_S57 |
+|  | 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 |
+|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
+| 0 | A0A075B6Q4 | 24 | S | True | 0.91 | 6.839384 | True | A0A075B6Q4_24 | 0.149257 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | VDDEKGDSNDDYDSA | A0A075B6Q4_S24 |
+| 1 | A0A075B6Q4 | 35 | S | True | 0.87 | 9.192622 | False | A0A075B6Q4_35 | 0.136966 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | YDSAGLLSDEDCMSV | A0A075B6Q4_S35 |
+| 2 | A0A075B6Q4 | 57 | S | False | 0.28 | 0.818834 | False | A0A075B6Q4_57 | 0.125364 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | IADHLFWSEETKSRF | A0A075B6Q4_S57 |
@@ -337,11 +362,12 @@ df.head(3)
 ```
-|     | gene  | protein     | uniprot | site | gene_site | SITE_GRP_ID | species | site_seq              | LT_LIT | MS_LIT | MS_CST | CST_CAT# | Ambiguous_Site |
-|-----|-------|-------------|---------|------|-----------|-------------|---------|-----------------------|--------|--------|--------|----------|----------------|
-| 0   | YWHAB | 14-3-3 beta | P31946  | T2   | YWHAB_T2  | 15718712    | human   | \_\_\_\_\_\_MtMDksELV | NaN    | 3.0    | 1.0    | None     | 0              |
-| 1   | YWHAB | 14-3-3 beta | P31946  | S6   | YWHAB_S6  | 15718709    | human   | \_\_MtMDksELVQkAk     | NaN    | 8.0    | NaN    | None     | 0              |
-| 2   | YWHAB | 14-3-3 beta | P31946  | Y21  | YWHAB_Y21 | 3426383     | human   | LAEQAERyDDMAAAM       | NaN    | NaN    | 4.0    | None     | 0              |
+|  | gene | protein | uniprot | site | gene_site | SITE_GRP_ID | species | site_seq | LT_LIT | MS_LIT | MS_CST | CST_CAT# | Ambiguous_Site |
+|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
+| 0 | YWHAB | 14-3-3 beta | P31946 | T2 | YWHAB_T2 | 15718712 | human | \_\_\_\_\_\_MtMDksELV | NaN | 3.0 | 1.0 | None | 0 |
+| 1 | YWHAB | 14-3-3 beta | P31946 | S6 | YWHAB_S6 | 15718709 | human | \_\_MtMDksELVQkAk | NaN | 8.0 | NaN | None | 0 |
+| 2 | YWHAB | 14-3-3 beta | P31946 | Y21 | YWHAB_Y21 | 3426383 | human | LAEQAERyDDMAAAM | NaN | NaN | 4.0 | None | 0 |
@@ -353,12 +379,14 @@ df.head(3)
 ```
-|     | site_seq        | gene_site  | gene  | source | num_site | acceptor | -7  | -6  | -5  | -4  | ... | -2  | -1  | 0   | 1   | 2   | 3   | 4   | 5   | 6   | 7   |
-|-----|-----------------|------------|-------|--------|----------|----------|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
-| 0   | AAAAAAASGGAGSDN | PBX1_S136  | PBX1  | ochoa  | 1        | S        | A   | A   | A   | A   | ... | A   | A   | S   | G   | G   | A   | G   | S   | D   | N   |
-| 1   | AAAAAAASGGGVSPD | PBX2_S146  | PBX2  | ochoa  | 1        | S        | A   | A   | A   | A   | ... | A   | A   | S   | G   | G   | G   | V   | S   | P   | D   |
-| 2   | AAAAAAASGVTTGKP | CLASR_S349 | CLASR | ochoa  | 1        | S        | A   | A   | A   | A   | ... | A   | A   | S   | G   | V   | T   | T   | G   | K   | P   |
+|  | site_seq | gene_site | gene | source | num_site | acceptor | -7 | -6 | -5 | -4 | ... | -2 | -1 | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
+|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
+| 0 | AAAAAAASGGAGSDN | PBX1_S136 | PBX1 | ochoa | 1 | S | A | A | A | A | ... | A | A | S | G | G | A | G | S | D | N |
+| 1 | AAAAAAASGGGVSPD | PBX2_S146 | PBX2 | ochoa | 1 | S | A | A | A | A | ... | A | A | S | G | G | G | V | S | P | D |
+| 2 | AAAAAAASGVTTGKP | CLASR_S349 | CLASR | ochoa | 1 | S | A | A | A | A | ... | A | A | S | G | V | T | T | G | K | P |
+<p>3 rows × 21 columns</p>
 ## Phosphorylation site sequence example

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@@ -3,9 +3,10 @@
 # See https://github.com/fastai/nbdev/blob/master/settings.ini for examples.
 ### Python library ###
-repo = python-katlas
-lib_name = %(repo)s
-version = 0.1.2
+repo = katlas
+#lib_name = %(repo)s
+lib_name = python-katlas
+version = 0.1.4
 min_python = 3.7
 license = apache2
 black_formatting = False

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1	- __version__ = "0.1.1"

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