python-katlas 0.1.3__tar.gz → 0.1.4__tar.gz

{python_katlas-0.1.3/python_katlas.egg-info → python_katlas-0.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: python-katlas
-Version: 0.1.3
+Version: 0.1.4
 Summary: tools for predicting kinome specificities
 Home-page: https://github.com/sky1ove/katlas
 Author: lily
@@ -44,10 +44,8 @@ Requires-Dist: openpyxl; extra == "dev"
 
 <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>
+<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
@@ -240,18 +238,7 @@ get_pct('AEEKEyHSEGG',**param_PSPA_y, pct_ref = y_pct)
 
     considering string: ['-5A', '-4E', '-3E', '-2K', '-1E', '0Y', '1H', '2S', '3E', '4G', '5G']
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 |       | log2(score) | percentile |
 |-------|-------------|------------|
@@ -268,7 +255,7 @@ get_pct('AEEKEyHSEGG',**param_PSPA_y, pct_ref = y_pct)
 | DDR2  | -4.920      | 10.403281  |
 
 <p>93 rows × 2 columns</p>
-</div>
+
 
 ## High-throughput substrate scoring on a dataframe
 
@@ -286,18 +273,7 @@ df = Data.get_ochoa_site().head()
 df.iloc[:,-2:]
 ```
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 |     | site_seq        | gene_site      |
 |-----|-----------------|----------------|
@@ -307,7 +283,7 @@ df.iloc[:,-2:]
 | 3   | KSRFTEYSMTSSVMR | A0A075B6Q4_S68 |
 | 4   | FTEYSMTSSVMRRNE | A0A075B6Q4_S71 |
 
-</div>
+
 
 ### Set the column name and param to calculate
 
@@ -326,18 +302,7 @@ results
 
     100%|██████████| 289/289 [00:05<00:00, 56.64it/s]
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 | kinase | SRC | EPHA3 | FES | NTRK3 | ALK | EPHA8 | ABL1 | FLT3 | EPHB2 | FYN | ... | MEK5 | PKN2 | MAP2K7 | MRCKB | HIPK3 | CDK8 | BUB1 | MEKK3 | MAP2K3 | GRK1 |
 |----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
@@ -348,7 +313,7 @@ results
 | 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>
-</div>
+
 
 ## Phosphorylation sites
 
@@ -362,18 +327,7 @@ df = Data.get_cptac_ensembl_site()
 df.head(3)
 ```
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 |  | gene | site | site_seq | protein | gene_name | gene_site | protein_site |
 |----|----|----|----|----|----|----|----|
@@ -381,7 +335,7 @@ df.head(3)
 | 1 | ENSG00000003056.8 | S267 | DDQLGEESEERDDHL | ENSP00000440488.2 | M6PR | M6PR_S267 | ENSP00000440488_S267 |
 | 2 | ENSG00000048028.11 | S1053 | PPTIRPNSPYDLCSR | ENSP00000003302.4 | USP28 | USP28_S1053 | ENSP00000003302_S1053 |
 
-</div>
+
 
 ### [Ochoa et al. human phosphoproteome](https://www.nature.com/articles/s41587-019-0344-3)
 
@@ -390,18 +344,7 @@ df = Data.get_ochoa_site()
 df.head(3)
 ```
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 |  | 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 |
 |----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
@@ -409,7 +352,7 @@ df.head(3)
 | 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 |
 
-</div>
+
 
 ### PhosphoSitePlus human phosphorylation site
 
@@ -418,18 +361,7 @@ df = Data.get_psp_human_site()
 df.head(3)
 ```
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 |  | gene | protein | uniprot | site | gene_site | SITE_GRP_ID | species | site_seq | LT_LIT | MS_LIT | MS_CST | CST_CAT# | Ambiguous_Site |
 |----|----|----|----|----|----|----|----|----|----|----|----|----|----|
@@ -437,7 +369,7 @@ df.head(3)
 | 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 |
 
-</div>
+
 
 ### Unique sites of combined Ochoa & PhosphoSitePlus
 
@@ -446,18 +378,7 @@ df = Data.get_combine_site_psp_ochoa()
 df.head(3)
 ```
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 |  | site_seq | gene_site | gene | source | num_site | acceptor | -7 | -6 | -5 | -4 | ... | -2 | -1 | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
 |----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
@@ -466,7 +387,7 @@ df.head(3)
 | 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>
-</div>
+
 
 ## Phosphorylation site sequence example
 

{python_katlas-0.1.3 → python_katlas-0.1.4}/README.md

@@ -5,10 +5,8 @@
 
 <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>
+<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
@@ -201,18 +199,7 @@ get_pct('AEEKEyHSEGG',**param_PSPA_y, pct_ref = y_pct)
 
     considering string: ['-5A', '-4E', '-3E', '-2K', '-1E', '0Y', '1H', '2S', '3E', '4G', '5G']
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 |       | log2(score) | percentile |
 |-------|-------------|------------|
@@ -229,7 +216,7 @@ get_pct('AEEKEyHSEGG',**param_PSPA_y, pct_ref = y_pct)
 | DDR2  | -4.920      | 10.403281  |
 
 <p>93 rows × 2 columns</p>
-</div>
+
 
 ## High-throughput substrate scoring on a dataframe
 
@@ -247,18 +234,7 @@ df = Data.get_ochoa_site().head()
 df.iloc[:,-2:]
 ```
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 |     | site_seq        | gene_site      |
 |-----|-----------------|----------------|
@@ -268,7 +244,7 @@ df.iloc[:,-2:]
 | 3   | KSRFTEYSMTSSVMR | A0A075B6Q4_S68 |
 | 4   | FTEYSMTSSVMRRNE | A0A075B6Q4_S71 |
 
-</div>
+
 
 ### Set the column name and param to calculate
 
@@ -287,18 +263,7 @@ results
 
     100%|██████████| 289/289 [00:05<00:00, 56.64it/s]
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 | kinase | SRC | EPHA3 | FES | NTRK3 | ALK | EPHA8 | ABL1 | FLT3 | EPHB2 | FYN | ... | MEK5 | PKN2 | MAP2K7 | MRCKB | HIPK3 | CDK8 | BUB1 | MEKK3 | MAP2K3 | GRK1 |
 |----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
@@ -309,7 +274,7 @@ results
 | 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>
-</div>
+
 
 ## Phosphorylation sites
 
@@ -323,18 +288,7 @@ df = Data.get_cptac_ensembl_site()
 df.head(3)
 ```
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 |  | gene | site | site_seq | protein | gene_name | gene_site | protein_site |
 |----|----|----|----|----|----|----|----|
@@ -342,7 +296,7 @@ df.head(3)
 | 1 | ENSG00000003056.8 | S267 | DDQLGEESEERDDHL | ENSP00000440488.2 | M6PR | M6PR_S267 | ENSP00000440488_S267 |
 | 2 | ENSG00000048028.11 | S1053 | PPTIRPNSPYDLCSR | ENSP00000003302.4 | USP28 | USP28_S1053 | ENSP00000003302_S1053 |
 
-</div>
+
 
 ### [Ochoa et al. human phosphoproteome](https://www.nature.com/articles/s41587-019-0344-3)
 
@@ -351,18 +305,7 @@ df = Data.get_ochoa_site()
 df.head(3)
 ```
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 |  | 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 |
 |----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
@@ -370,7 +313,7 @@ df.head(3)
 | 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 |
 
-</div>
+
 
 ### PhosphoSitePlus human phosphorylation site
 
@@ -379,18 +322,7 @@ df = Data.get_psp_human_site()
 df.head(3)
 ```
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 |  | gene | protein | uniprot | site | gene_site | SITE_GRP_ID | species | site_seq | LT_LIT | MS_LIT | MS_CST | CST_CAT# | Ambiguous_Site |
 |----|----|----|----|----|----|----|----|----|----|----|----|----|----|
@@ -398,7 +330,7 @@ df.head(3)
 | 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 |
 
-</div>
+
 
 ### Unique sites of combined Ochoa & PhosphoSitePlus
 
@@ -407,18 +339,7 @@ df = Data.get_combine_site_psp_ochoa()
 df.head(3)
 ```
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 |  | site_seq | gene_site | gene | source | num_site | acceptor | -7 | -6 | -5 | -4 | ... | -2 | -1 | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
 |----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
@@ -427,7 +348,7 @@ df.head(3)
 | 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>
-</div>
+
 
 ## Phosphorylation site sequence example
 

python_katlas-0.1.4/katlas/__init__.py

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

{python_katlas-0.1.3 → python_katlas-0.1.4}/katlas/plot.py

@@ -266,7 +266,7 @@ 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 37
@@ -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', 
@@ -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
@@ -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)

{python_katlas-0.1.3 → python_katlas-0.1.4/python_katlas.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: python-katlas
-Version: 0.1.3
+Version: 0.1.4
 Summary: tools for predicting kinome specificities
 Home-page: https://github.com/sky1ove/katlas
 Author: lily
@@ -44,10 +44,8 @@ Requires-Dist: openpyxl; extra == "dev"
 
 <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>
+<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
@@ -240,18 +238,7 @@ get_pct('AEEKEyHSEGG',**param_PSPA_y, pct_ref = y_pct)
 
     considering string: ['-5A', '-4E', '-3E', '-2K', '-1E', '0Y', '1H', '2S', '3E', '4G', '5G']
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 |       | log2(score) | percentile |
 |-------|-------------|------------|
@@ -268,7 +255,7 @@ get_pct('AEEKEyHSEGG',**param_PSPA_y, pct_ref = y_pct)
 | DDR2  | -4.920      | 10.403281  |
 
 <p>93 rows × 2 columns</p>
-</div>
+
 
 ## High-throughput substrate scoring on a dataframe
 
@@ -286,18 +273,7 @@ df = Data.get_ochoa_site().head()
 df.iloc[:,-2:]
 ```
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 |     | site_seq        | gene_site      |
 |-----|-----------------|----------------|
@@ -307,7 +283,7 @@ df.iloc[:,-2:]
 | 3   | KSRFTEYSMTSSVMR | A0A075B6Q4_S68 |
 | 4   | FTEYSMTSSVMRRNE | A0A075B6Q4_S71 |
 
-</div>
+
 
 ### Set the column name and param to calculate
 
@@ -326,18 +302,7 @@ results
 
     100%|██████████| 289/289 [00:05<00:00, 56.64it/s]
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 | kinase | SRC | EPHA3 | FES | NTRK3 | ALK | EPHA8 | ABL1 | FLT3 | EPHB2 | FYN | ... | MEK5 | PKN2 | MAP2K7 | MRCKB | HIPK3 | CDK8 | BUB1 | MEKK3 | MAP2K3 | GRK1 |
 |----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
@@ -348,7 +313,7 @@ results
 | 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>
-</div>
+
 
 ## Phosphorylation sites
 
@@ -362,18 +327,7 @@ df = Data.get_cptac_ensembl_site()
 df.head(3)
 ```
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 |  | gene | site | site_seq | protein | gene_name | gene_site | protein_site |
 |----|----|----|----|----|----|----|----|
@@ -381,7 +335,7 @@ df.head(3)
 | 1 | ENSG00000003056.8 | S267 | DDQLGEESEERDDHL | ENSP00000440488.2 | M6PR | M6PR_S267 | ENSP00000440488_S267 |
 | 2 | ENSG00000048028.11 | S1053 | PPTIRPNSPYDLCSR | ENSP00000003302.4 | USP28 | USP28_S1053 | ENSP00000003302_S1053 |
 
-</div>
+
 
 ### [Ochoa et al. human phosphoproteome](https://www.nature.com/articles/s41587-019-0344-3)
 
@@ -390,18 +344,7 @@ df = Data.get_ochoa_site()
 df.head(3)
 ```
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 |  | 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 |
 |----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
@@ -409,7 +352,7 @@ df.head(3)
 | 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 |
 
-</div>
+
 
 ### PhosphoSitePlus human phosphorylation site
 
@@ -418,18 +361,7 @@ df = Data.get_psp_human_site()
 df.head(3)
 ```
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 |  | gene | protein | uniprot | site | gene_site | SITE_GRP_ID | species | site_seq | LT_LIT | MS_LIT | MS_CST | CST_CAT# | Ambiguous_Site |
 |----|----|----|----|----|----|----|----|----|----|----|----|----|----|
@@ -437,7 +369,7 @@ df.head(3)
 | 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 |
 
-</div>
+
 
 ### Unique sites of combined Ochoa & PhosphoSitePlus
 
@@ -446,18 +378,7 @@ df = Data.get_combine_site_psp_ochoa()
 df.head(3)
 ```
 
-<div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-&#10;    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-&#10;    .dataframe thead th {
-        text-align: right;
-    }
-</style>
+
 
 |  | site_seq | gene_site | gene | source | num_site | acceptor | -7 | -6 | -5 | -4 | ... | -2 | -1 | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
 |----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|
@@ -466,7 +387,7 @@ df.head(3)
 | 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>
-</div>
+
 
 ## Phosphorylation site sequence example
 

{python_katlas-0.1.3 → python_katlas-0.1.4}/settings.ini

@@ -6,7 +6,7 @@
 repo = katlas
 #lib_name = %(repo)s
 lib_name = python-katlas
-version = 0.1.3
+version = 0.1.4
 min_python = 3.7
 license = apache2
 black_formatting = False

python_katlas-0.1.3/katlas/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.1.2"