added cbioportal, pfam, and utils_requests; ran black and flake8 on e… (

#5)

* added cbioportal, pfam, and utils_requests; ran black and flake8 on everything in src for the first time

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.codecov.yml

@@ -11,4 +11,4 @@ comment:
   branches: null
   behavior: default
   flags: null
-  paths: null
+  paths: null

.github/CONTRIBUTING.md

@@ -1,7 +1,7 @@
 # How to contribute
 
 We welcome contributions from external contributors, and this document
-describes how to merge code changes into this missense_kinase_toolkit. 
+describes how to merge code changes into this missense_kinase_toolkit.
 
 ## Getting Started
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -9,4 +9,4 @@ Notable points that this PR has either accomplished or will accomplish.
 - [ ] Question1
 
 ## Status
-- [ ] Ready to go
+- [ ] Ready to go

.pre-commit-config.yaml

@@ -32,4 +32,4 @@ repos:
   hooks:
   - id: pyupgrade
     args:
-    - --py39-plus
+    - --py39-plus

README.md

@@ -14,6 +14,6 @@ Copyright (c) 2024, Jess White
 
 
 #### Acknowledgements
- 
-Project based on the 
+
+Project based on the
 [Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.1.

data/README.md

@@ -1,7 +1,7 @@
 # Sample Package Data
 
 This directory contains sample additional data you may want to include with your package.
-This is a place where non-code related additional information (such as data files, molecular structures,  etc.) can 
+This is a place where non-code related additional information (such as data files, molecular structures,  etc.) can
 go that you want to ship alongside your code.
 
 Please note that it is not recommended to place large files in your git directory. If your project requires files larger

devtools/README.md

@@ -1,14 +1,14 @@
 # Development, testing, and deployment tools
 
-This directory contains a collection of tools for running Continuous Integration (CI) tests, 
+This directory contains a collection of tools for running Continuous Integration (CI) tests,
 conda installation, and other development tools not directly related to the coding process.
 
 
 ## Manifest
 
 ### Continuous Integration
 
-You should test your code, but do not feel compelled to use these specific programs. You also may not need Unix and 
+You should test your code, but do not feel compelled to use these specific programs. You also may not need Unix and
 Windows testing if you only plan to deploy on specific platforms. These are just to help you get started.
 
 ### Conda Environment:
@@ -17,7 +17,7 @@ This directory contains the files to setup the Conda environment for testing pur
 
 * `conda-envs`: directory containing the YAML file(s) which fully describe Conda Environments, their dependencies, and those dependency provenance's
   * `test_env.yaml`: Simple test environment file with base dependencies. Channels are not specified here and therefore respect global Conda configuration
-  
+
 ### Additional Scripts:
 
 This directory contains OS agnostic helper scripts which don't fall in any of the previous categories
@@ -40,17 +40,17 @@ This directory contains OS agnostic helper scripts which don't fall in any of th
 - [ ] Make sure there is an/are issue(s) opened for your specific update
 - [ ] Create the PR, referencing the issue
 - [ ] Debug the PR as needed until tests pass
-- [ ] Tag the final, debugged version 
+- [ ] Tag the final, debugged version
    *  `git tag -a X.Y.Z [latest pushed commit] && git push --follow-tags`
 - [ ] Get the PR merged in
 
 ## Versioneer Auto-version
-[Versioneer](https://github.com/warner/python-versioneer) will automatically infer what version 
-is installed by looking at the `git` tags and how many commits ahead this version is. The format follows 
+[Versioneer](https://github.com/warner/python-versioneer) will automatically infer what version
+is installed by looking at the `git` tags and how many commits ahead this version is. The format follows
 [PEP 440](https://www.python.org/dev/peps/pep-0440/) and has the regular expression of:
 ```regexp
 \d+.\d+.\d+(?\+\d+-[a-z0-9]+)
 ```
-If the version of this commit is the same as a `git` tag, the installed version is the same as the tag, 
-e.g. `missense_kinase_toolkit-0.1.2`, otherwise it will be appended with `+X` where `X` is the number of commits 
+If the version of this commit is the same as a `git` tag, the installed version is the same as the tag,
+e.g. `missense_kinase_toolkit-0.1.2`, otherwise it will be appended with `+X` where `X` is the number of commits
 ahead from the last tag, and then `-YYYYYY` where the `Y`'s are replaced with the `git` commit hash.

devtools/conda-envs/test_env.yaml

@@ -17,4 +17,3 @@ dependencies:
     # Pip-only installs
   #- pip:
   #  - codecov
-

devtools/scripts/create_conda_env.py

@@ -28,7 +28,7 @@
         except (KeyError, ImportError, IndexError):
             raise ImportError("No YAML parser could be found in this or the conda environment. "
                               "Could not find PyYAML or Ruamel YAML in the current environment, "
-                              "AND could not find Ruamel YAML in the base conda environment through CONDA_EXE path. " 
+                              "AND could not find Ruamel YAML in the base conda environment through CONDA_EXE path. "
                               "Environment not created!")
     loader = yaml.YAML(typ="safe").load  # typ="safe" avoids odd typing on output
 
@@ -57,10 +57,10 @@ def temp_cd():
 args = parser.parse_args()
 
 # Open the base file
-with open(args.conda_file, "r") as handle:
+with open(args.conda_file) as handle:
     yaml_script = loader(handle.read())
 
-python_replacement_string = "python {}*".format(args.python)
+python_replacement_string = f"python {args.python}*"
 
 try:
     for dep_index, dep_value in enumerate(yaml_script['dependencies']):
@@ -82,14 +82,14 @@ def temp_cd():
 if conda_path is None:
     raise RuntimeError("Could not find a conda binary in CONDA_EXE variable or in executable search path")
 
-print("CONDA ENV NAME  {}".format(args.name))
-print("PYTHON VERSION  {}".format(args.python))
-print("CONDA FILE NAME {}".format(args.conda_file))
-print("CONDA PATH      {}".format(conda_path))
+print(f"CONDA ENV NAME  {args.name}")
+print(f"PYTHON VERSION  {args.python}")
+print(f"CONDA FILE NAME {args.conda_file}")
+print(f"CONDA PATH      {conda_path}")
 
 # Write to a temp directory which will always be cleaned up
 with temp_cd():
     temp_file_name = "temp_script.yaml"
     with open(temp_file_name, 'w') as f:
         f.write(yaml.dump(yaml_script))
-    sp.call("{} env create -n {} -f {}".format(conda_path, args.name, temp_file_name), shell=True)
+    sp.call(f"{conda_path} env create -n {args.name} -f {temp_file_name}", shell=True)

docs/Makefile

@@ -17,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/README.md

@@ -5,7 +5,7 @@ To compile the docs, first ensure that Sphinx and the ReadTheDocs theme are inst
 
 
 ```bash
-conda install sphinx sphinx_rtd_theme 
+conda install sphinx sphinx_rtd_theme
 ```
 
 
@@ -14,11 +14,10 @@ Once installed, you can use the `Makefile` in this directory to compile static H
 make html
 ```
 
-The compiled docs will be in the `_build` directory and can be viewed by opening `index.html` (which may itself 
+The compiled docs will be in the `_build` directory and can be viewed by opening `index.html` (which may itself
 be inside a directory called `html/` depending on what version of Sphinx is installed).
 
 
 A configuration file for [Read The Docs](https://readthedocs.org/) (readthedocs.yaml) is included in the top level of the repository. To use Read the Docs to host your documentation, go to https://readthedocs.org/ and connect this repository. You may need to change your default branch to `main` under Advanced Settings for the project.
 
 If you would like to use Read The Docs with `autodoc` (included automatically) and your package has dependencies, you will need to include those dependencies in your documentation yaml file (`docs/requirements.yaml`).
-

docs/_static/README.md

@@ -1,11 +1,11 @@
 # Static Doc Directory
 
 Add any paths that contain custom static files (such as style sheets) here,
-relative to the `conf.py` file's directory. 
+relative to the `conf.py` file's directory.
 They are copied after the builtin static files,
 so a file named "default.css" will overwrite the builtin "default.css".
 
-The path to this folder is set in the Sphinx `conf.py` file in the line: 
+The path to this folder is set in the Sphinx `conf.py` file in the line:
 ```python
 templates_path = ['_static']
 ```

docs/_templates/README.md

@@ -1,11 +1,11 @@
 # Templates Doc Directory
 
-Add any paths that contain templates here, relative to  
+Add any paths that contain templates here, relative to
 the `conf.py` file's directory.
 They are copied after the builtin template files,
 so a file named "page.html" will overwrite the builtin "page.html".
 
-The path to this folder is set in the Sphinx `conf.py` file in the line: 
+The path to this folder is set in the Sphinx `conf.py` file in the line:
 ```python
 html_static_path = ['_templates']
 ```

docs/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Configuration file for the Sphinx documentation builder.
 #

docs/getting_started.rst

@@ -1,4 +1,4 @@
 Getting Started
 ===============
 
-This page details how to get started with missense-kinase-toolkit. 
+This page details how to get started with missense-kinase-toolkit.

docs/requirements.yaml

@@ -9,4 +9,3 @@ dependencies:
 
     # Pip-only installs
   #- pip:
-

readthedocs.yml

@@ -12,4 +12,4 @@ python:
       path: .
 
 conda:
-  environment: docs/requirements.yaml
+  environment: docs/requirements.yaml

src/missense_kinase_toolkit/cbioportal.py

@@ -0,0 +1,145 @@
+from __future__ import annotations
+
+import re
+
+import requests
+import pandas as pd
+
+
+def create_setlist(
+    input_object: requests.models.Response,
+    attr: str,
+) -> tuple[list, set]:
+    """Create a list and set of unique values from a response object
+
+    Parameters
+    ----------
+    input_object : requests.models.Response
+        Response object from a request
+    attr : str
+        Attribute to extract from the response object
+
+    Returns
+    -------
+    tuple[list, set]
+        List and set of unique values from the response object
+    """
+    list_output = []
+    set_output = set()
+
+    for entry in input_object:
+        list_output.append(entry[attr])
+        set_output.add(entry[attr])
+
+    return list_output, set_output
+
+
+def print_counts(
+    list_input: list,
+) -> None:
+    """Print the counts of unique values in a list
+
+    Parameters
+    ----------
+    list_input : list
+        List of values to count
+
+    Returns
+    -------
+    None
+    """
+    for Unique in set(list_input):
+        n = list_input.count(Unique)
+        print(f"{Unique:<15} \t {n:>10}")
+
+
+def parse_obj2dict(
+    input_object: requests.models.Response,
+) -> dict:
+    """Parse a response object into a dictionary
+
+    Parameters
+    ----------
+    input_object : requests.models.Response
+        Response object from a request
+
+    Returns
+    -------
+    dict
+        Dictionary of values from the response object
+    """
+    dict_output = {}
+
+    list_dir = dir(input_object[0])
+
+    for attr in list_dir:
+        list_attr = []
+        for entry in input_object:
+            try:
+                add = int(entry[attr])
+            except ValueError:
+                add = str(entry[attr])
+            list_attr.append(add)
+        dict_output[attr] = list_attr
+
+    return dict_output
+
+
+def parse_series2dict(
+    series: pd.Series,
+    strwrap: None | str = None,
+    delim1: None | str = None,
+    delim2: None | str = None,
+) -> dict:
+    """Parse a series into a dictionary
+
+    Parameters
+    ----------
+    series : pd.Series
+        Series to parse
+    strwrap : None | str
+        Regular expression to wrap the values in the series
+    delim1 : None | str
+        Delimiter to split the values in the series
+    delim2 : None | str
+        Delimiter to split the values in the series
+
+    Returns
+    -------
+    dict
+        Dictionary of values from the series
+    """
+    if strwrap is None:
+        strwrap = r"Gene\((.*)\)"
+    if delim1 is None:
+        delim1 = ", "
+    if delim2 is None:
+        delim2 = "="
+
+    list_temp = series.apply(
+        lambda x: re.search(strwrap, str(x)).group(1).split(delim1)
+    )
+    list_keys = [gene.split(delim2)[0] for gene in list_temp[0]]
+    dict_out = {key: [] for key in list_keys}
+
+    for row in list_temp:
+        list_row = [col.split(delim2)[1] for col in row]
+        for idx, col in enumerate(list_row):
+            dict_out[list_keys[idx]].append(col)
+
+    return dict_out
+
+
+def calc_vaf(
+    dataframe,
+    alt: None | str = None,
+    ref: None | str = None,
+):
+    if alt is None:
+        alt = "tumorAltCount"
+    if ref is None:
+        ref = "tumorRefCount"
+
+    vaf = dataframe[alt] / (dataframe[alt] + dataframe[ref])
+
+    return vaf