python-katlas 0.1.3__tar.gz → 0.2.0__tar.gz

{python_katlas-0.1.3/python_katlas.egg-info → python_katlas-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: python-katlas
-Version: 0.1.3
+Version: 0.2.0
 Summary: tools for predicting kinome specificities
 Home-page: https://github.com/sky1ove/katlas
 Author: lily
@@ -18,36 +18,52 @@ Classifier: License :: OSI Approved :: Apache Software License
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: pandas
+Requires-Dist: gdown
 Requires-Dist: statsmodels
+Requires-Dist: statannotations
 Requires-Dist: fastparquet
+Requires-Dist: pyarrow
 Requires-Dist: tqdm
+Requires-Dist: logomaker-kinase
+Requires-Dist: seaborn
+Requires-Dist: bokeh
+Requires-Dist: reactome2py
+Requires-Dist: adjustText
+Requires-Dist: scikit-learn
+Requires-Dist: umap-learn
+Requires-Dist: ipywidgets
+Requires-Dist: biopython
 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: fastai; 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"
+Requires-Dist: transformers; extra == "dev"
+Requires-Dist: sentencepiece; extra == "dev"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 # KATLAS
 
 
 <!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
 
-<img alt="Katlas logo" width="600" caption="Katlas logo" src="https://github.com/sky1ove/katlas/raw/main/dataset/images/logo.png" id="logo"/>
-
-<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>
+<img alt="Katlas logo" width="600" caption="Katlas logo" src="https://github.com/sky1ove/katlas/raw/main/logo.png" id="logo"/>
 
 KATLAS is a repository containing python tools to predict kinases given
 a substrate sequence. It also contains datasets of kinase substrate
@@ -83,8 +99,6 @@ helpful to your research.
 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
@@ -93,26 +107,27 @@ code.
 Check out our latest web platform:
 [kinase-atlas.com](https://kinase-atlas.com/)
 
-## Tutorials on Colab
+## Install
 
-- 1.  [Substrate scoring on a single substrate
-      sequence](https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/tutorial_01_sinlge_input.ipynb)
-- 2.  [High throughput substrate scoring on phosphoproteomics
-      dataset](https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/tutorial_02_high_throughput.ipynb)
-- 3.  [Kinase enrichment analysis for AKT
-      inhibitor](https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/tutorial_03a_enrichment_AKTi.ipynb)
+UV:
 
-## Install
+``` bash
+uv add -U python-katlas
+```
 
-    pip install python-katlas -U
+pip:
 
-To use other modules besides the core, do
-`pip install 'python-katlas[dev]' -U`
+``` bash
+pip install -U python-katlas
+```
+
+If using machine-learning related modules, need to install development
+verison: `pip install -U "python-katlas[dev]"`
 
 ## Import
 
 ``` python
-from katlas.core import *
+from katlas.common import *
 ```
 
 # Quick start
@@ -132,93 +147,101 @@ For input sequences, we also consider it in two conditions:
 - all capital
 - contains lower cases indicating phosphorylation status
 
-## Single sequence as input
+## Quick start
+
+### Site scoring
 
-### CDDM, all capital
+CDDM, all capital
 
 ``` python
-predict_kinase('AAAAAAASGGAGSDN',**param_CDDM_upper)
+predict_kinase('AAAAAAASGAGSDN',**Params("CDDM_upper"))
 ```
 
-    considering string: ['-7A', '-6A', '-5A', '-4A', '-3A', '-2A', '-1A', '0S', '1G', '2G', '3A', '4G', '5S', '6D', '7N']
+    considering string: ['-7A', '-6A', '-5A', '-4A', '-3A', '-2A', '-1A', '0S', '1G', '2A', '3G', '4S', '5D', '6N']
 
-    kinase
-    PAK6     2.032
-    ULK3     2.032
-    PRKX     2.012
-    ATR      1.991
-    PRKD1    1.988
-             ...  
-    DDR2     0.928
-    EPHA4    0.928
-    TEK      0.921
-    KIT      0.915
-    FGFR3    0.910
-    Length: 289, dtype: float64
+    GCN2      4.556
+    MPSK1     4.425
+    MEKK2     4.253
+    WNK3      4.213
+    WNK1      4.064
+              ...  
+    PDK1    -25.077
+    PDHK3   -25.346
+    CLK2    -27.251
+    ROR2    -27.582
+    DDR1    -53.581
+    Length: 328, dtype: float64
 
-### CDDM, with lower case indicating phosphorylation status
+CDDM, with lower case indicating phosphorylation status
 
 ``` python
-predict_kinase('AAAAAAAsGGAGsDN',**param_CDDM)
+predict_kinase('AAAAAAAsGGAGsDN',**Params("CDDM"))
 ```
 
     considering string: ['-7A', '-6A', '-5A', '-4A', '-3A', '-2A', '-1A', '0s', '1G', '2G', '3A', '4G', '5s', '6D', '7N']
 
-    kinase
-    ULK3     1.987
-    PAK6     1.981
-    PRKD1    1.946
-    PIM3     1.944
-    PRKX     1.939
-             ...  
-    EPHA4    0.905
-    EGFR     0.900
-    TEK      0.898
-    FGFR3    0.894
-    KIT      0.882
-    Length: 289, dtype: float64
-
-### PSPA, with lower case indicating phosphorylation status
+    ROR1       8.355
+    WNK1       4.907
+    WNK2       4.782
+    ERK5       4.466
+    RIPK2      4.045
+               ...  
+    DDR1     -29.393
+    TNNI3K   -29.884
+    CHAK1    -31.775
+    VRK1     -45.287
+    BRAF     -49.403
+    Length: 328, dtype: float64
+
+PSPA, with lower case indicating phosphorylation status
 
 ``` python
-predict_kinase('AEEKEyHsEGG',**param_PSPA).head()
+predict_kinase('AEEKEyHsEGG',**Params("PSPA"))
 ```
 
     considering string: ['-5A', '-4E', '-3E', '-2K', '-1E', '0y', '1H', '2s', '3E', '4G', '5G']
 
     kinase
-    EGFR     4.013
-    FGFR4    3.568
-    ZAP70    3.412
-    CSK      3.241
-    SYK      3.209
-    dtype: float64
-
-### To replicate the results from The Kinase Library (PSPA)
+    EGFR          4.013
+    FGFR4         3.568
+    ZAP70         3.412
+    CSK           3.241
+    SYK           3.209
+                  ...  
+    JAK1         -3.837
+    DDR2         -4.421
+    TNK2         -4.534
+    TNNI3K_TYR   -4.651
+    TNK1         -5.320
+    Length: 93, dtype: float64
+
+To replicate the results from The Kinase Library (PSPA)
 
 Check this link: [The Kinase
-Library](https://kinase-library.phosphosite.org/site?s=AEEKEy*HsEGG&pp=false&scp=true),
+Library](https://kinase-library.mit.edu/site?s=AEEKEy*HSEGG&pp=false&scp=true),
 and use log2(score) to rank, it shows same results with the below (with
 slight differences due to rounding).
 
 ``` python
-predict_kinase('AEEKEyHSEGG',**param_PSPA).head(10)
+out = predict_kinase('AEEKEyHSEGG',**Params("PSPA"))
+out
 ```
 
     considering string: ['-5A', '-4E', '-3E', '-2K', '-1E', '0y', '1H', '2S', '3E', '4G', '5G']
 
     kinase
-    EGFR         3.181
-    FGFR4        2.390
-    CSK          2.308
-    ZAP70        2.068
-    SYK          1.998
-    PDHK1_TYR    1.922
-    RET          1.732
-    MATK         1.688
-    FLT1         1.627
-    BMPR2_TYR    1.456
-    dtype: float64
+    EGFR     3.181
+    FGFR4    2.390
+    CSK      2.308
+    ZAP70    2.068
+    SYK      1.998
+             ...  
+    EPHA1   -3.501
+    FES     -3.699
+    TNK1    -4.269
+    TNK2    -4.577
+    DDR2    -4.920
+    Length: 93, dtype: float64
 
 - So far [The kinase Library](https://kinase-library.phosphosite.org)
   considers all ***tyr sequences*** in capital regardless of whether or
@@ -234,8 +257,10 @@ sheet.
 ``` python
 # Percentile reference sheet
 y_pct = Data.get_pspa_tyr_pct()
+```
 
-get_pct('AEEKEyHSEGG',**param_PSPA_y, pct_ref = y_pct)
+``` python
+get_pct('AEEKEyHSEGG',pct_ref = y_pct,**Params("PSPA_y"))
 ```
 
     considering string: ['-5A', '-4E', '-3E', '-2K', '-1E', '0Y', '1H', '2S', '3E', '4G', '5G']
@@ -270,15 +295,15 @@ get_pct('AEEKEyHSEGG',**param_PSPA_y, pct_ref = y_pct)
 <p>93 rows × 2 columns</p>
 </div>
 
-## High-throughput substrate scoring on a dataframe
+### Site scoring in a df
 
-### Load your csv
+Load your csv:
 
 ``` python
 # df = pd.read_csv('your_file.csv')
 ```
 
-### Load a demo df
+Or load a demo df
 
 ``` python
 # Load a demo df with phosphorylation sites
@@ -309,22 +334,21 @@ df.iloc[:,-2:]
 
 </div>
 
-### Set the column name and param to calculate
+Set the column name and param to calculate
 
 Here we choose param_CDDM_upper, as the sequences in the demo df are all
 in capital. You can also choose other params.
 
 ``` python
-results = predict_kinase_df(df,'site_seq',**param_CDDM_upper)
+results = predict_kinase_df(df,'site_seq',**Params("CDDM_upper"))
 results
 ```
 
     input dataframe has a length 5
     Preprocessing
     Finish preprocessing
-    Calculating position: [-7, -6, -5, -4, -3, -2, -1, 0, 1, 2, 3, 4, 5, 6, 7]
-
-    100%|██████████| 289/289 [00:05<00:00, 56.64it/s]
+    Merging reference
+    Finish merging
 
 <div>
 <style scoped>
@@ -339,18 +363,35 @@ results
     }
 </style>
 
-| kinase | SRC | EPHA3 | FES | NTRK3 | ALK | EPHA8 | ABL1 | FLT3 | EPHB2 | FYN | ... | MEK5 | PKN2 | MAP2K7 | MRCKB | HIPK3 | CDK8 | BUB1 | MEKK3 | MAP2K3 | GRK1 |
+|  | SRC | EPHA3 | FES | NTRK3 | ALK | ABL1 | FLT3 | EPHA8 | EPHB2 | EPHB1 | ... | VRK1 | PKMYT1 | GRK3 | CAMK1B | CDC7 | SMMLCK | ROR1 | GAK | MAST2 | BRAF |
 |----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
-| 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 |
+| 0 | -2.440640 | -0.818753 | -1.663990 | -0.738991 | -2.047628 | -3.602344 | -3.200998 | -0.935176 | -1.388444 | -1.859450 | ... | -17.103237 | -113.698143 | -16.848783 | -41.520172 | -41.646187 | 1.284159 | -26.566362 | -69.165062 | -17.706400 | -87.763214 |
+| 1 | -3.838486 | -2.735969 | -2.533986 | -2.150399 | -3.792498 | -4.725527 | -5.711791 | -4.534240 | -3.148449 | -2.511518 | ... | -67.889053 | -68.652641 | -45.833855 | -64.171600 | -39.465572 | -65.061722 | -109.561707 | -85.911224 | -60.105064 | -63.889122 |
+| 2 | -2.610423 | -2.370090 | -3.235637 | -1.508413 | -2.571347 | -3.740941 | -3.025596 | -3.373504 | -2.776297 | -3.060740 | ... | -15.798462 | -45.905319 | -61.440742 | -67.695694 | -55.047962 | -42.135216 | -38.501572 | -62.624382 | -56.119389 | -107.060989 |
+| 3 | -5.180541 | -4.201880 | -5.766463 | -3.038421 | -3.836897 | -4.249900 | -5.029885 | -5.411311 | -4.713308 | -4.827825 | ... | -96.978317 | -83.419777 | -22.559393 | -110.611588 | -63.283070 | -37.240440 | -24.497492 | -112.878151 | -43.538158 | -60.348518 |
+| 4 | -2.844254 | -3.322700 | -3.681745 | -1.766435 | -2.666579 | -3.748774 | -4.083619 | -3.912834 | -3.724181 | -3.948160 | ... | -35.824612 | -87.983566 | -83.312317 | -107.162407 | -61.478374 | -85.793571 | -43.738819 | -47.004211 | -42.281624 | -59.518513 |
 
-<p>5 rows × 289 columns</p>
+<p>5 rows × 328 columns</p>
 </div>
 
-## Phosphorylation sites
+``` python
+results.iloc[0].sort_values(ascending=False)
+```
+
+    TLK2        8.264621
+    GCN2        8.101542
+    TLK1        7.693897
+    HRI         6.691402
+    PLK3        6.579368
+                 ...    
+    NIK       -64.605148
+    SRPK2     -67.300667
+    GAK       -69.165062
+    BRAF      -87.763214
+    PKMYT1   -113.698143
+    Name: 0, Length: 328, dtype: float32
+
+## Dataset
 
 Besides calculating sequence scores, we also provides multiple datasets
 of phosphorylation sites.
@@ -405,9 +446,9 @@ 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 |
+| 0 | A0A075B6Q4 | 24 | S | 1.0 | 0.91 | 6.839384 | 1.0 | A0A075B6Q4_24 | 0.149257 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | VDDEKGDSNDDYDSA | A0A075B6Q4_S24 |
+| 1 | A0A075B6Q4 | 35 | S | 1.0 | 0.87 | 9.192622 | 0.0 | A0A075B6Q4_35 | 0.136966 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | YDSAGLLSDEDCMSV | A0A075B6Q4_S35 |
+| 2 | A0A075B6Q4 | 57 | S | 0.0 | 0.28 | 0.818834 | 0.0 | A0A075B6Q4_57 | 0.125364 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | IADHLFWSEETKSRF | A0A075B6Q4_S57 |
 
 </div>
 
@@ -459,13 +500,12 @@ df.head(3)
     }
 </style>
 
-|  | 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 |
+|  | uniprot | gene | site | site_seq | source | AM_pathogenicity | CDDM_upper | CDDM_max_score |
+|----|----|----|----|----|----|----|----|----|
+| 0 | A0A024R4G9 | C19orf48 | S20 | ITGSRLLSMVPGPAR | psp | NaN | PRKX,AKT1,PKG1,P90RSK,HIPK4,AKT3,HIPK1,PKACB,H... | 2.407041 |
+| 1 | A0A075B6Q4 | None | S24 | VDDEKGDSNDDYDSA | ochoa | NaN | CK2A2,CK2A1,GRK7,GRK5,CK1G1,CK1A,IKKA,CK1G2,CA... | 2.295654 |
+| 2 | A0A075B6Q4 | None | S35 | YDSAGLLSDEDCMSV | ochoa | NaN | CK2A2,CK2A1,IKKA,ATM,IKKB,CAMK1D,MARK2,GRK7,IK... | 2.488683 |
 
-<p>3 rows × 21 columns</p>
 </div>
 
 ## Phosphorylation site sequence example