diff --git a/.github/workflows/CI.yaml b/.github/workflows/databases-ci.yaml similarity index 76% rename from .github/workflows/CI.yaml rename to .github/workflows/databases-ci.yaml index 9a9c7dd..3a544c2 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/databases-ci.yaml @@ -1,4 +1,4 @@ -name: CI +name: databases-ci on: # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming @@ -6,9 +6,13 @@ on: push: branches: - "main" + paths: + - "missense_kinase_toolkit/databases/**" pull_request: branches: - "main" + paths: + - "missense_kinase_toolkit/databases/**" schedule: # Weekly tests run on main by default: # Scheduled workflows run on the latest commit on the default or base branch. @@ -27,9 +31,6 @@ jobs: steps: - uses: actions/checkout@v3 - # - name: Install poetry - # run: pipx install poetry - - name: Additional info about the build shell: bash run: | @@ -45,7 +46,6 @@ jobs: environment-name: test # conda-forge is the default channel now and does not need to be specified channels: conda-forge,defaults - # cache: 'poetry' extra-specs: | python=${{ matrix.python-version }} @@ -53,29 +53,28 @@ jobs: # conda setup requires this special shell shell: bash -l {0} run: | - python -m pip install . --no-deps - # python -m pip install poetry - # python -m venv .venv --copies - # poetry config virtualenvs.create false - # poetry install + python -m pip install ./missense_kinase_toolkit/databases --no-deps micromamba list - name: Run tests # conda setup requires this special shell shell: bash -l {0} run: | - pytest -v --cov=missense_kinase_toolkit --cov-report=xml --color=yes tests/ - # poetry run pytest -v --cov=missense_kinase_toolkit --cov-report=xml --color=yes tests/ + # run each package test suite; append to coverage file + # exit immediately if a command exits with a non-zero status + set -e + # pytest -n auto --durations=10 -v --cov-report=xml --cov-report=term --color=yes \ + pytest -v --cov-report=xml --color=yes \ + --cov=missense_kinase_toolkit/databases \ + missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/tests/ - name: Upload coverage reports to Codecov uses: codecov/codecov-action@v4.0.1 with: fail_ci_if_error: false # optional (default = false) file: ./coverage.xml - flags: unittests # optional + flags: databases # optional name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} # https://github.com/codecov/codecov-action token: ${{ secrets.CODECOV_TOKEN }} # required verbose: true # optional (default = false) - # env: - # slug: choderalab/missense-kinase-toolkit diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml index 7210450..ba8a138 100644 --- a/devtools/conda-envs/test_env.yaml +++ b/devtools/conda-envs/test_env.yaml @@ -14,11 +14,7 @@ dependencies: - pytest-cov - codecov - # Pip-only installs - #- pip: - # - codecov - - # Other + # Databases - pandas - bravado - requests-cache diff --git a/docs/getting_started.rst b/docs/getting_started.rst index 40eea54..ea93d54 100644 --- a/docs/getting_started.rst +++ b/docs/getting_started.rst @@ -1,19 +1,21 @@ Getting Started =============== -This page details how to get started with missense-kinase-toolkit. +This page details how to get started with missense-kinase-toolkit. We have used a monorepo structure where all sub-packages are contained within the `missense-kinase-toolkit` sub-directory. Installation ++++++++++++ +To install the `databases` sub-package using a virtual environment: + .. code-block:: bash git clone https://github.com/choderalab/missense-kinase-toolkit.git - cd missense-kinase-toolkit + cd missense-kinase-toolkit/missense-kinase-toolkit/databases python3 -m venv VE source VE/bin/activate - pip install -e '.[test,extras]' + python3 -m pip install -e '.[dev,test]' -Alternatively, since we have used `poetry` as our default package manager for this project. Once you have cloned the repository and have either installed `poetry` locally or in your environment of interest, you can install the package by running the following command in the root directory of the repository using the provided `poetry.lock` file and the following command +Alternatively, since we have used `poetry` as our default package manager for this project. Once you have cloned the repository and have either installed `poetry` locally or in your environment of interest, you can install the package by running the following command in the root directory of the sub-package repository using the provided `poetry.lock` file and the following command .. code-block:: bash diff --git a/missense_kinase_toolkit/databases/README.md b/missense_kinase_toolkit/databases/README.md new file mode 100644 index 0000000..77ae1af --- /dev/null +++ b/missense_kinase_toolkit/databases/README.md @@ -0,0 +1 @@ +# databases diff --git a/tests/__init__.py b/missense_kinase_toolkit/databases/missense_kinase_toolkit/__init__.py similarity index 100% rename from tests/__init__.py rename to missense_kinase_toolkit/databases/missense_kinase_toolkit/__init__.py diff --git a/src/missense_kinase_toolkit/databases/__init__.py b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/__init__.py similarity index 68% rename from src/missense_kinase_toolkit/databases/__init__.py rename to missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/__init__.py index dd870a4..764b4dd 100644 --- a/src/missense_kinase_toolkit/databases/__init__.py +++ b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/__init__.py @@ -2,4 +2,4 @@ from importlib.metadata import version -__version__ = version("missense-kinase-toolkit") +__version__ = version("databases") diff --git a/src/missense_kinase_toolkit/databases/api_schema.py b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/api_schema.py similarity index 84% rename from src/missense_kinase_toolkit/databases/api_schema.py rename to missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/api_schema.py index db5cdbc..d25a9d2 100644 --- a/src/missense_kinase_toolkit/databases/api_schema.py +++ b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/api_schema.py @@ -1,4 +1,5 @@ -from abc import abstractmethod, ABC +from abc import ABC, abstractmethod + from bravado.client import SwaggerClient from bravado.requests_client import RequestsClient @@ -15,9 +16,7 @@ class SwaggerAPIClient(ABC): @abstractmethod - def query_api( - self - ) -> SwaggerClient: + def query_api(self) -> SwaggerClient: """Query a Swagger API and return result. Parameters @@ -35,9 +34,7 @@ def query_api( class APIKeySwaggerClient(SwaggerAPIClient, ABC): @abstractmethod - def maybe_get_token( - self - ) -> str | None: + def maybe_get_token(self) -> str | None: """Get API token, if available. Returns @@ -48,9 +45,7 @@ def maybe_get_token( """ ... - def set_api_key( - self - ) -> RequestsClient: + def set_api_key(self) -> RequestsClient: """Set API key for cBioPortal API. Returns @@ -66,7 +61,7 @@ def set_api_key( self.instance, f"Bearer {token}", param_name="Authorization", - param_in="header" + param_in="header", ) else: print("No API token provided") @@ -75,5 +70,4 @@ def set_api_key( class RESTAPIClient(ABC): @abstractmethod - def query_api(self): - ... + def query_api(self): ... diff --git a/src/missense_kinase_toolkit/databases/cbioportal.py b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/cbioportal.py similarity index 89% rename from src/missense_kinase_toolkit/databases/cbioportal.py rename to missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/cbioportal.py index da83d26..55bb03b 100644 --- a/src/missense_kinase_toolkit/databases/cbioportal.py +++ b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/cbioportal.py @@ -1,18 +1,20 @@ import logging + import pandas as pd from bravado.client import SwaggerClient -# from pydantic import BaseModel as PydanticBaseModel -# from dataclasses import dataclass +from missense_kinase_toolkit.databases.api_schema import APIKeySwaggerClient from missense_kinase_toolkit.databases.config import ( get_cbioportal_instance, - maybe_get_cbioportal_token + maybe_get_cbioportal_token, ) from missense_kinase_toolkit.databases.io_utils import ( parse_iterabc2dataframe, save_dataframe_to_csv, ) -from missense_kinase_toolkit.databases.api_schema import APIKeySwaggerClient + +# from pydantic import BaseModel as PydanticBaseModel +# from dataclasses import dataclass logger = logging.getLogger(__name__) @@ -20,6 +22,7 @@ class cBioPortal(APIKeySwaggerClient): """Class to interact with the cBioPortal API.""" + def __init__(self): """Initialize cBioPortal Class object. @@ -51,8 +54,8 @@ def query_api(self): config={ "validate_requests": False, "validate_responses": False, - "validate_swagger_spec": False - } + "validate_swagger_spec": False, + }, ) return cbioportal_api @@ -72,6 +75,7 @@ def get_cbioportal(self): class Mutations(cBioPortal): """Class to get mutations from a cBioPortal study.""" + def __init__( self, study_id: str, @@ -110,20 +114,22 @@ def get_all_mutations_by_study( study_ids = [study.studyId for study in studies] if self.study_id in study_ids: - #TODO: add incremental error handling beyond missing study + # TODO: add incremental error handling beyond missing study muts = self._cbioportal.Mutations.getMutationsInMolecularProfileBySampleListIdUsingGET( molecularProfileId=f"{self.study_id}_mutations", sampleListId=f"{self.study_id}_all", - projection="DETAILED" - ).result() + projection="DETAILED", + ).result() else: - logging.error(f"Study {self.study_id} not found in cBioPortal instance {self.instance}") + logging.error( + f"Study {self.study_id} not found in cBioPortal instance {self.instance}" + ) return muts def get_cbioportal_cohort_mutations( self, - bool_save = False, + bool_save=False, ) -> None: """Get cBioPortal cohort mutations and optionally save as a CSV file. @@ -135,7 +141,8 @@ def get_cbioportal_cohort_mutations( Notes ----- The CSV file will be saved in the output directory specified in the configuration file. - As the "gene" ABC object is nested within the "mutation" ABC object, the two dataframes are parsed and concatenated. + As the "gene" ABC object is nested within the "mutation" ABC object, + the two dataframes are parsed and concatenated. """ df_muts = parse_iterabc2dataframe(self._mutations) @@ -157,4 +164,5 @@ def get_mutations(self): """Get cBioPortal mutations.""" return self._mutations -#TODO: implement clinical annotations class + +# TODO: implement clinical annotations class diff --git a/src/missense_kinase_toolkit/databases/colors.py b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/colors.py similarity index 59% rename from src/missense_kinase_toolkit/databases/colors.py rename to missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/colors.py index 1fef66e..e061c07 100644 --- a/src/missense_kinase_toolkit/databases/colors.py +++ b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/colors.py @@ -70,7 +70,7 @@ def map_single_letter_aa_to_color(aa, dict_color): if aa_clean is None: print(f"{aa} is an invalid amino acid; using '-' as default symbol.") aa_clean = "-" - if aa_clean in dict_color.keys(): + if aa_clean in dict_color.keys(): return dict_color[aa_clean] else: print(f"Invalid amino acid: {aa}") @@ -102,68 +102,68 @@ def map_single_letter_aa_to_color(aa, dict_color): DICT_COLORS = { # https://en.wikipedia.org/wiki/Help:Distinguishable_colors - "ALPHABET_PROJECT" : { - "DICT_COLORS" : { - "-" : "#FFFFFF", - "A" : "#F0A3FF", - "B" : "#0075DC", - "C" : "#993F00", - "D" : "#4C005C", - "E" : "#191919", - "F" : "#005C31", - "G" : "#2BCE48", - "H" : "#FFCC99", - "I" : "#808080", - "J" : "#94FFB5", - "K" : "#8F7C00", - "L" : "#9DCC00", - "M" : "#C20088", - "N" : "#003380", - "O" : "#FFA405", - "P" : "#FFA8BB", - "Q" : "#426600", - "R" : "#FF0010", - "S" : "#5EF1F2", - "T" : "#00998F", - "U" : "#E0FF66", - "V" : "#740AFF", - "W" : "#990000", - "X" : "#FFFF80", - "Y" : "#FFE100", - "Z" : "#FF5005" + "ALPHABET_PROJECT": { + "DICT_COLORS": { + "-": "#FFFFFF", + "A": "#F0A3FF", + "B": "#0075DC", + "C": "#993F00", + "D": "#4C005C", + "E": "#191919", + "F": "#005C31", + "G": "#2BCE48", + "H": "#FFCC99", + "I": "#808080", + "J": "#94FFB5", + "K": "#8F7C00", + "L": "#9DCC00", + "M": "#C20088", + "N": "#003380", + "O": "#FFA405", + "P": "#FFA8BB", + "Q": "#426600", + "R": "#FF0010", + "S": "#5EF1F2", + "T": "#00998F", + "U": "#E0FF66", + "V": "#740AFF", + "W": "#990000", + "X": "#FFFF80", + "Y": "#FFE100", + "Z": "#FF5005", }, - "DICT_ANNOTATION" : None + "DICT_ANNOTATION": None, }, # asapdiscovery-genetics/asapdiscovery/genetics/seq_alignment.py - "ASAP" : { - "DICT_COLORS" : { - "A": "red", # Alanine (ALA) - "R": "blue", # Arginine (ARG) - "N": "green", # Asparagine (ASN) - "D": "yellow", # Aspartic acid (ASP) - "C": "orange", # Cysteine (CYS) - "Q": "purple", # Glutamine (GLN) - "E": "cyan", # Glutamic acid (GLU) - "G": "magenta", # Glycine (GLY) - "H": "pink", # Histidine (HIS) - "I": "brown", # Isoleucine (ILE) - "L": "gray", # Leucine (LEU) - "K": "lime", # Lysine (LYS) - "M": "teal", # Methionine (MET) - "F": "navy", # Phenylalanine (PHE) - "P": "olive", # Proline (PRO) - "S": "maroon", # Serine (SER) - "T": "silver", # Threonine (THR) - "W": "gold", # Tryptophan (TRP) - "Y": "skyblue", # Tyrosine (TYR) - "V": "violet", # Valine (VAL) + "ASAP": { + "DICT_COLORS": { + "A": "red", # Alanine (ALA) + "R": "blue", # Arginine (ARG) + "N": "green", # Asparagine (ASN) + "D": "yellow", # Aspartic acid (ASP) + "C": "orange", # Cysteine (CYS) + "Q": "purple", # Glutamine (GLN) + "E": "cyan", # Glutamic acid (GLU) + "G": "magenta", # Glycine (GLY) + "H": "pink", # Histidine (HIS) + "I": "brown", # Isoleucine (ILE) + "L": "gray", # Leucine (LEU) + "K": "lime", # Lysine (LYS) + "M": "teal", # Methionine (MET) + "F": "navy", # Phenylalanine (PHE) + "P": "olive", # Proline (PRO) + "S": "maroon", # Serine (SER) + "T": "silver", # Threonine (THR) + "W": "gold", # Tryptophan (TRP) + "Y": "skyblue", # Tyrosine (TYR) + "V": "violet", # Valine (VAL) "-": "white", }, - "DICT_ANNOTATION" : None + "DICT_ANNOTATION": None, }, # http://openrasmol.org/doc/rasmol.html#aminocolours - "RASMOL" : { - "DICT_COLORS" : { + "RASMOL": { + "DICT_COLORS": { "A": "#C8C8C8", # Alanine (ALA) "R": "#145AFF", # Arginine (ARG) "N": "#00DCDC", # Asparagine (ASN) @@ -186,27 +186,26 @@ def map_single_letter_aa_to_color(aa, dict_color): "V": "#0F820F", # Valine (VAL) "-": "#BEA06E", }, - "DICT_ANNOTATION" : { - - "A" : "#C8C8C8", - "R, K" : "#145AFF", - "N, Q" : "#00DCDC", - "D, E" : "#E60A0A", - "C, M" : "#E6E600", - "G" : "#EBEBEB", - "H" : "#8282D2", - "I, L, V" : "#0F820F", - "F, Y" : "#3232AA", - "P" : "#DC9682", - "S, T" : "#FA9600", - "W" : "#B45AB4", - "-" : "#BEA06E", - } + "DICT_ANNOTATION": { + "A": "#C8C8C8", + "R, K": "#145AFF", + "N, Q": "#00DCDC", + "D, E": "#E60A0A", + "C, M": "#E6E600", + "G": "#EBEBEB", + "H": "#8282D2", + "I, L, V": "#0F820F", + "F, Y": "#3232AA", + "P": "#DC9682", + "S, T": "#FA9600", + "W": "#B45AB4", + "-": "#BEA06E", + }, }, # http://openrasmol.org/doc/rasmol.html#shapelycolours # https://www.dnastar.com/manuals/MegAlignPro/17.3.1/en/topic/change-the-analysis-view-color-scheme - "SHAPELY" : { - "DICT_COLORS" : { + "SHAPELY": { + "DICT_COLORS": { "A": "#8CFF8C", # Alanine (ALA) "R": "#00007C", # Arginine (ARG) "N": "#FF7C70", # Asparagine (ASN) @@ -229,61 +228,61 @@ def map_single_letter_aa_to_color(aa, dict_color): "V": "#004C00", # Valine (VAL) "-": "#000000", }, - "DICT_ANNOTATION" : { - "A" : "#8CFF8C", - "R, K" : "#00007C", - "N, Q" : "#FF7C70", - "D, E" : "#A00042", - "C, M" : "#FFFF70", - "G" : "#FFFFFF", - "H" : "#7070FF", - "I, L, V" : "#004C00", - "F, Y" : "#534C42", - "P" : "#525252", - "S, T" : "#FF7042", - "W" : "#4F4600", - "-" : "#000000", - } + "DICT_ANNOTATION": { + "A": "#8CFF8C", + "R, K": "#00007C", + "N, Q": "#FF7C70", + "D, E": "#A00042", + "C, M": "#FFFF70", + "G": "#FFFFFF", + "H": "#7070FF", + "I, L, V": "#004C00", + "F, Y": "#534C42", + "P": "#525252", + "S, T": "#FF7042", + "W": "#4F4600", + "-": "#000000", + }, }, # https://www.jalview.org/help/html/colourSchemes/clustal.html - "CLUSTALX" : { - "DICT_COLORS" : { - "A": "blue", # Alanine (ALA) - "R": "red", # Arginine (ARG) - "N": "green", # Asparagine (ASN) - "D": "magenta", # Aspartic acid (ASP) - "C": "pink", # Cysteine (CYS) - "Q": "green", # Glutamine (GLN) - "E": "magenta", # Glutamic acid (GLU) + "CLUSTALX": { + "DICT_COLORS": { + "A": "blue", # Alanine (ALA) + "R": "red", # Arginine (ARG) + "N": "green", # Asparagine (ASN) + "D": "magenta", # Aspartic acid (ASP) + "C": "pink", # Cysteine (CYS) + "Q": "green", # Glutamine (GLN) + "E": "magenta", # Glutamic acid (GLU) "G": "orange", # Glycine (GLY) - "H": "cyan", # Histidine (HIS) - "I": "blue", # Isoleucine (ILE) - "L": "blue", # Leucine (LEU) - "K": "red", # Lysine (LYS) - "M": "blue", # Methionine (MET) - "F": "blue", # Phenylalanine (PHE) + "H": "cyan", # Histidine (HIS) + "I": "blue", # Isoleucine (ILE) + "L": "blue", # Leucine (LEU) + "K": "red", # Lysine (LYS) + "M": "blue", # Methionine (MET) + "F": "blue", # Phenylalanine (PHE) "P": "yellow", # Proline (PRO) - "S": "green", # Serine (SER) - "T": "green", # Threonine (THR) - "W": "blue", # Tryptophan (TRP) - "Y": "cyan", # Tyrosine (TYR) - "V": "blue", # Valine (VAL) + "S": "green", # Serine (SER) + "T": "green", # Threonine (THR) + "W": "blue", # Tryptophan (TRP) + "Y": "cyan", # Tyrosine (TYR) + "V": "blue", # Valine (VAL) "-": "white", }, - "DICT_ANNOTATION" : { + "DICT_ANNOTATION": { "hydrophobic": "blue", # A,I,L,M,F,W,V - "positive": "red", # K,R + "positive": "red", # K,R "negative": "magenta", # D,E - "polar": "green", # N,Q,S,T - "aromatic": "cyan", # H,Y - "cysteine": "pink", # C - "glycine": "orange", # G - "proline": "yellow", # P - } + "polar": "green", # N,Q,S,T + "aromatic": "cyan", # H,Y + "cysteine": "pink", # C + "glycine": "orange", # G + "proline": "yellow", # P + }, }, # https://www.jalview.org/help/html/colourSchemes/zappo.html - "ZAPPO" : { - "DICT_COLORS" : { + "ZAPPO": { + "DICT_COLORS": { "A": "#ffafaf", # Alanine (ALA) "R": "#6464ff", # Arginine (ARG) "N": "#02ff00", # Asparagine (ASN) @@ -306,16 +305,16 @@ def map_single_letter_aa_to_color(aa, dict_color): "V": "#ffafaf", # Valine (VAL) "-": "#000000", }, - "DICT_ANNOTATION" : { - "aliphatic hydrophobic" : "#ffafaf", # A,I,L,M,V - "aromatic" : "#ffc803", # F,W,Y - "positive" : "#6464ff", # R,H,K - "negative" : "#ff0000", # D,E - "hydrophilic" : "#02ff00", # N,Q,S,T - "conformationally special" : "#ff00ff", # G,P - "cysteine" : "#ffff00", # C - } - } + "DICT_ANNOTATION": { + "aliphatic hydrophobic": "#ffafaf", # A,I,L,M,V + "aromatic": "#ffc803", # F,W,Y + "positive": "#6464ff", # R,H,K + "negative": "#ff0000", # D,E + "hydrophilic": "#02ff00", # N,Q,S,T + "conformationally special": "#ff00ff", # G,P + "cysteine": "#ffff00", # C + }, + }, } """dict[dict[str, str], dict[str, str]]: Mapping amino acid to color using specified dictionary. Dictionaries include color schemes from: diff --git a/src/missense_kinase_toolkit/databases/config.py b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/config.py similarity index 72% rename from src/missense_kinase_toolkit/databases/config.py rename to missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/config.py index 7c6be1b..975e87b 100644 --- a/src/missense_kinase_toolkit/databases/config.py +++ b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/config.py @@ -1,20 +1,19 @@ import os import sys - OUTPUT_DIR_VAR = "OUTPUT_DIR" """str: Environment variable for output directory""" CBIOPORTAL_INSTANCE_VAR = "CBIOPORTAL_INSTANCE" -"""str: Environment variable for cBioPortal instance; if none provided, default is `www.cbioportal.org` in CLI scripts""" +"""str: Environment variable for cBioPortal instance; \ + if none provided, default is `www.cbioportal.org` in CLI scripts""" CBIOPORTAL_TOKEN_VAR = "CBIOPORTAL_TOKEN" """str: Environment variable for cBioPortal token; if none provided, default is `None` in CLI scripts""" REQUESTS_CACHE_VAR = "REQUESTS_CACHE" -"""str: Environment variable for request cache file prefix; if none provided, default is requests_cache in CLI scripts""" +"""str: Environment variable for request cache file prefix; \ + if none provided, default is requests_cache in CLI scripts""" -def set_output_dir( - val: str -) -> None: +def set_output_dir(val: str) -> None: """Set the output directory in environment variables. Parameters @@ -30,8 +29,7 @@ def set_output_dir( os.environ[OUTPUT_DIR_VAR] = val -def get_output_dir( -) -> str | None: +def get_output_dir() -> str | None: """Get the output directory from the environment. Returns @@ -42,13 +40,13 @@ def get_output_dir( try: return os.environ[OUTPUT_DIR_VAR] except KeyError: - print("Output directory not found in environment variables. This is necessary to run analysis. Exiting...") + print( + "Output directory not found in environment variables. This is necessary to run analysis. Exiting..." + ) sys.exit(1) -def set_cbioportal_instance( - val: str -) -> None: +def set_cbioportal_instance(val: str) -> None: """Set the cBioPortal instance in the environment variables. Parameters @@ -64,8 +62,7 @@ def set_cbioportal_instance( os.environ[CBIOPORTAL_INSTANCE_VAR] = val -def get_cbioportal_instance( -) -> str | None: +def get_cbioportal_instance() -> str | None: """Get the cBioPortal instance from the environment. Returns @@ -76,13 +73,13 @@ def get_cbioportal_instance( try: return os.environ[CBIOPORTAL_INSTANCE_VAR] except KeyError: - print("cBioPortal instance not found in environment variables. This is necessary to run analysis. Exiting...") + print( + "cBioPortal instance not found in environment variables. This is necessary to run analysis. Exiting..." + ) sys.exit(1) -def set_cbioportal_token( - val: str -) -> None: +def set_cbioportal_token(val: str) -> None: """Set the cBioPortal token in the environment variables. Parameters @@ -98,8 +95,7 @@ def set_cbioportal_token( os.environ[CBIOPORTAL_TOKEN_VAR] = val -def maybe_get_cbioportal_token( -) -> str | None: +def maybe_get_cbioportal_token() -> str | None: """Get the cBioPortal token from the environment. Returns @@ -113,9 +109,7 @@ def maybe_get_cbioportal_token( return None -def set_request_cache( - val: str -) -> None: +def set_request_cache(val: str) -> None: """Set the request cache path in environment variables. Parameters @@ -131,8 +125,7 @@ def set_request_cache( os.environ[REQUESTS_CACHE_VAR] = val -def maybe_get_request_cache( -) -> str | None: +def maybe_get_request_cache() -> str | None: """Get the request cache path from the environment. Returns diff --git a/src/missense_kinase_toolkit/databases/hgnc.py b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/hgnc.py similarity index 84% rename from src/missense_kinase_toolkit/databases/hgnc.py rename to missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/hgnc.py index 7fd244a..1eb40f6 100644 --- a/src/missense_kinase_toolkit/databases/hgnc.py +++ b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/hgnc.py @@ -1,16 +1,19 @@ -import requests import logging +import requests + from missense_kinase_toolkit.databases import requests_wrapper, utils_requests logger = logging.getLogger(__name__) + class HGNC: """Class to interact with the HGNC API.""" + def __init__( - self, - input_symbol_or_id: str, - input_is_hgnc_symbol: bool = True, + self, + input_symbol_or_id: str, + input_is_hgnc_symbol: bool = True, ) -> None: """Initialize HGNC Class object. @@ -49,7 +52,8 @@ def maybe_get_symbol_from_hgnc_search( Parameters ---------- custom_field : str | None - Optional: custom field to search for in the HGNC REST API; otherwise defaults to "symbol" or "ensembl_gene_id" + Optional: custom field to search for in the HGNC REST API; \ + otherwise defaults to "symbol" or "ensembl_gene_id" See https://www.genenames.org/help/rest/ under "searchableFields" for options custom_term : str | None Optional: custom term to search for in the HGNC REST API @@ -69,17 +73,22 @@ def maybe_get_symbol_from_hgnc_search( url = f"{self.url}/search/ensembl_gene_id:{self.ensembl}" res = requests_wrapper.get_cached_session().get( - url, - headers={"Accept": "application/json"} + url, headers={"Accept": "application/json"} ) if res.ok: - list_hgnc_gene_name = self._extract_list_from_hgnc_response_docs(res, "symbol") + list_hgnc_gene_name = self._extract_list_from_hgnc_response_docs( + res, "symbol" + ) if len(list_hgnc_gene_name) == 1: if self.hgnc is not None: - print(f"Gene name found for {self.hgnc}: {list_hgnc_gene_name[0]}. Overwriting HGNC gene name...") + print( + f"Gene name found for {self.hgnc}: {list_hgnc_gene_name[0]}. Overwriting HGNC gene name..." + ) else: - print(f"Gene name found for {self.ensembl}: {list_hgnc_gene_name[0]}. Adding HGNC gene name...") + print( + f"Gene name found for {self.ensembl}: {list_hgnc_gene_name[0]}. Adding HGNC gene name..." + ) self.hgnc = list_hgnc_gene_name[0] elif len(list_hgnc_gene_name) == 0: print(f"No gene names found for {self.hgnc}") @@ -111,7 +120,8 @@ def maybe_get_info_from_hgnc_fetch( Notes ----- - The list of extractable fields can be found at https://www.genenames.org/help/rest/ under "storedFields" in the JSON or XML outputs. + The list of extractable fields can be found at https://www.genenames.org/help/rest/ \ + under "storedFields" in the JSON or XML outputs. """ if self.hgnc is not None: @@ -130,7 +140,9 @@ def maybe_get_info_from_hgnc_fetch( if entry not in set_keys: list_out.append(None) else: - list_entry = self._extract_list_from_hgnc_response_docs(res, entry) + list_entry = self._extract_list_from_hgnc_response_docs( + res, entry + ) list_out.append(list_entry) else: list_out = [None for _ in list_to_extract] @@ -139,7 +151,10 @@ def maybe_get_info_from_hgnc_fetch( dict_out = dict(zip(list_to_extract, list_out)) else: - print("No HGNC gene symbol provided; cannot fetch gene information from HGNC API with Ensembl gene ID {self.ensembl}") + print( + "No HGNC gene symbol provided; cannot fetch gene information \ + from HGNC API with Ensembl gene ID {self.ensembl}" + ) dict_out = None return dict_out @@ -190,7 +205,9 @@ def _generate_key_set_hgnc_response_docs( """ try: - list_keys = [set(doc.keys()) for doc in res_input.json()["response"]["docs"]] + list_keys = [ + set(doc.keys()) for doc in res_input.json()["response"]["docs"] + ] set_keys = set.union(*list_keys) except TypeError: set_keys = set() diff --git a/src/missense_kinase_toolkit/databases/io_utils.py b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/io_utils.py similarity index 96% rename from src/missense_kinase_toolkit/databases/io_utils.py rename to missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/io_utils.py index 6033a46..75eb211 100644 --- a/src/missense_kinase_toolkit/databases/io_utils.py +++ b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/io_utils.py @@ -1,13 +1,12 @@ import os -import pandas as pd +import pandas as pd OUTPUT_DIR_VAR = "OUTPUT_DIR" """str: Environment variable for output directory""" -def check_outdir_exists( -) -> str: +def check_outdir_exists() -> str: """Check if OUTPUT_DIR in environmental variables and create directory if doesn't exist. Returns @@ -25,9 +24,7 @@ def check_outdir_exists( return path_data -def convert_str2list( - input_str: str -) -> list[str]: +def convert_str2list(input_str: str) -> list[str]: """Convert a string to a list. Parameters @@ -126,7 +123,7 @@ def concatenate_csv_files_with_glob( else: print(f"No files matching {str_find} found in {path_data}...") - #TODO: implement remove duplicates + # TODO: implement remove duplicates return df_combo diff --git a/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/kinase_schema.py b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/kinase_schema.py new file mode 100644 index 0000000..9826145 --- /dev/null +++ b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/kinase_schema.py @@ -0,0 +1,60 @@ +from dataclasses import dataclass + +# TODO create a Pydantic model to incorporate and UniProt, Pfam, and KLIFS data for all +# eventually populate with AF2 active BLAminus+ structures from Dunbrack lab + + +# TODO: Make Pydantic model instead of dataclass +@dataclass +class KLIFSPocket: + """Dataclass to hold KLIFS pocket alignment information per kinase. + + Attributes + ---------- + uniprotID : str + UniProt ID + hgncName : str + HGNC name + uniprotSeq : str + UniProt canonical sequence + klifsSeq : str + KLIFS pocket sequence + list_klifs_region : list[str] + List of start and end regions of KLIFS pocket separated by ":"; end region will be the + same as start region if no concatenation necessary to find a single exact match + list_klifs_substr_actual : list[str] + List of substring of KLIFS pocket that maps to the *start region* of the KLIFS pocket + list_klifs_substr_match : list[str] + List of the actual substring used to match to the KLIFS pocket for the region(s) provided; + will be the same as list_klifs_substr_actual if no concatenation necessary to find a single exact match + list_substring_idxs : list[list[int] | None] + List of indices in UniProt sequence where KLIFS substring match starts; + offset by length of preceding KLIFS region with gaps removed + + """ + + uniprotID: str + hgncName: str + uniprotSeq: str + klifsSeq: str + list_klifs_region: list[str] + list_klifs_substr_actual: list[str] + list_klifs_substr_match: list[str] + list_substring_idxs: list[list[int] | None] + + def remove_klifs_list_gaps(self): + """Remove gaps from KLIFS pocket substring list. + + Returns + ------- + list_substring_klifs_narm = list[str] + List of KLIFS pocket substrings with gaps removed + + """ + from missense_kinase_toolkit.databases.klifs import remove_gaps_from_klifs + + list_substring_klifs_narm = [ + remove_gaps_from_klifs(substring_klifs) + for substring_klifs in self.list_klifs_substring + ] + return list_substring_klifs_narm diff --git a/src/missense_kinase_toolkit/databases/klifs.py b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/klifs.py similarity index 71% rename from src/missense_kinase_toolkit/databases/klifs.py rename to missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/klifs.py index b409f07..016a7e4 100644 --- a/src/missense_kinase_toolkit/databases/klifs.py +++ b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/klifs.py @@ -1,11 +1,10 @@ -import numpy as np import logging +import numpy as np from bravado.client import SwaggerClient from missense_kinase_toolkit.databases.api_schema import SwaggerAPIClient - logger = logging.getLogger(__name__) @@ -100,8 +99,7 @@ """list[tuple[int, str]]: Mapping KLIFS pocket ID to region""" -def convert_pocket_region_list_to_dict( -) -> dict[str, dict[str, int]]: +def convert_pocket_region_list_to_dict() -> dict[str, dict[str, int]]: """Convert list of pocket regions to dictionary. Returns @@ -124,121 +122,64 @@ def convert_pocket_region_list_to_dict( list_klifs_start = list(np.array(list_klifs_start)[idx_sort]) list_klifs_end = list(np.array(list_klifs_end)[idx_sort]) - dict_klifs_regions = {region : {"start" : list_klifs_start[idx], - "end" : list_klifs_end[idx]} for idx, region in enumerate(list_klifs_region)} + dict_klifs_regions = { + region: {"start": list_klifs_start[idx], "end": list_klifs_end[idx]} + for idx, region in enumerate(list_klifs_region) + } return dict_klifs_regions DICT_POCKET_KLIFS_REGIONS = { - "I": { - "start": 1, - "end": 3 - }, - "g.l": { - "start": 4, - "end": 9 - }, - "II": { - "start": 10, - "end": 13 - }, - "III": { - "start": 14, - "end": 19 - }, - "αC": { - "start": 20, - "end": 30 - }, - "b.l": { - "start": 31, - "end": 37 - }, - "IV": { - "start": 38, - "end": 41 - }, - "V": { - "start": 42, - "end": 44 - }, - "GK": { - "start": 45, - "end": 45 - }, - "hinge": { - "start": 46, - "end": 48 - }, - "linker": { - "start": 49, - "end": 52 - }, - "αD": { - "start": 53, - "end": 59 - }, - "αE": { - "start": 60, - "end": 64 - }, - "VI": { - "start": 65, - "end": 67 - }, - "c.l": { - "start": 68, - "end": 75 - }, - "VII": { - "start": 76, - "end": 78 - }, - "VIII": { - "start": 79, - "end": 79 - }, - "xDFG": { - "start": 80, - "end": 83 - }, - "a.l": { - "start": 84, - "end": 85 - } + "I": {"start": 1, "end": 3}, + "g.l": {"start": 4, "end": 9}, + "II": {"start": 10, "end": 13}, + "III": {"start": 14, "end": 19}, + "αC": {"start": 20, "end": 30}, + "b.l": {"start": 31, "end": 37}, + "IV": {"start": 38, "end": 41}, + "V": {"start": 42, "end": 44}, + "GK": {"start": 45, "end": 45}, + "hinge": {"start": 46, "end": 48}, + "linker": {"start": 49, "end": 52}, + "αD": {"start": 53, "end": 59}, + "αE": {"start": 60, "end": 64}, + "VI": {"start": 65, "end": 67}, + "c.l": {"start": 68, "end": 75}, + "VII": {"start": 76, "end": 78}, + "VIII": {"start": 79, "end": 79}, + "xDFG": {"start": 80, "end": 83}, + "a.l": {"start": 84, "end": 85}, } """dict[str, dict[str, int]]: Mapping KLIFS pocket region to start and end indices""" # courtesy of OpenCADD POCKET_KLIFS_REGION_COLORS = { - "I" : "khaki", - "g.l" : "green", - "II" : "khaki", - "III" : "khaki", - "αC" : "red", - "b.l" : "green", - "IV" : "khaki", - "V" : "khaki", - "GK" : "orange", - "hinge" : "magenta", - "linker" : "cyan", - "αD" : "red", - "αE" : "red", - "VI" : "khaki", - "c.l" : "darkorange", - "VII" : "khaki", - "VIII" : "khaki", - "xDFG" : "cornflowerblue", - "a.l" : "cornflowerblue", + "I": "khaki", + "g.l": "green", + "II": "khaki", + "III": "khaki", + "αC": "red", + "b.l": "green", + "IV": "khaki", + "V": "khaki", + "GK": "orange", + "hinge": "magenta", + "linker": "cyan", + "αD": "red", + "αE": "red", + "VI": "khaki", + "c.l": "darkorange", + "VII": "khaki", + "VIII": "khaki", + "xDFG": "cornflowerblue", + "a.l": "cornflowerblue", } """dict[str, str]: Mapping KLIFS pocket region to color""" -def remove_gaps_from_klifs( - klifs_string: str -) -> str: +def remove_gaps_from_klifs(klifs_string: str) -> str: """Remove gaps from KLIFS pocket sequence. Parameters @@ -257,9 +198,8 @@ def remove_gaps_from_klifs( def return_idx_of_substring_in_superstring( - superstring: str, - substring: str - ) -> list[int] | None: + superstring: str, substring: str +) -> list[int] | None: """ Parameters @@ -275,17 +215,19 @@ def return_idx_of_substring_in_superstring( Index where substring begins in superstring; None if substring not in superstring """ - list_out = [i for i in range(len(superstring)) if superstring.startswith(substring, i)] + list_out = [ + i for i in range(len(superstring)) if superstring.startswith(substring, i) + ] return list_out def align_klifs_pocket_to_uniprot_seq( - idx_start: int, - idx_end: int, - str_uniprot: str, - str_klifs: str, - ) -> list[int] | None: - """ Align KLIFS region to UniProt canonical Uniprot sequence. + idx_start: int, + idx_end: int, + str_uniprot: str, + str_klifs: str, +) -> list[int] | None: + """Align KLIFS region to UniProt canonical Uniprot sequence. Parameters ---------- @@ -311,17 +253,19 @@ def align_klifs_pocket_to_uniprot_seq( if len(substring_klifs_narm) == 0: list_idx = None else: - list_idx = return_idx_of_substring_in_superstring(str_uniprot, substring_klifs_narm) + list_idx = return_idx_of_substring_in_superstring( + str_uniprot, substring_klifs_narm + ) return substring_klifs, list_idx -#TODO "b.l" algorithm since non-contiguous region -#TODO keep match string separate from KLIFS substring at start region +# TODO "b.l" algorithm since non-contiguous region +# TODO keep match string separate from KLIFS substring at start region def iterate_klifs_alignment( string_uniprot: str, string_klifs: str, ) -> dict[str, list[str | list[int] | None]]: - """ Align KLIFS region to UniProt canonical Uniprot sequence. + """Align KLIFS region to UniProt canonical Uniprot sequence. Parameters ---------- @@ -341,7 +285,7 @@ def iterate_klifs_alignment( List of substring of KLIFS pocket that maps to the *start region* of the KLIFS pocket list_klifs_substr_match : list[str] List of the actual substring used to match to the KLIFS pocket for the region(s) provided; - will be the same as list_klifs_substr_actual if no concatenation necessary to find a single exact match + same as list_klifs_substr_actual if no concatenation necessary to find a single exact match list_substring_idxs : list[list[int | None]] List of indices in UniProt sequence where KLIFS region starts @@ -356,14 +300,16 @@ def iterate_klifs_alignment( for klifs_index, klifs_region in enumerate(list_klifs): klifs_region_start, klifs_region_end = klifs_region, klifs_region - klifs_idx_start, klifs_idx_end = dict_klifs[klifs_region_start]["start"]-1, \ - dict_klifs[klifs_region_end]["end"] + klifs_idx_start, klifs_idx_end = ( + dict_klifs[klifs_region_start]["start"] - 1, + dict_klifs[klifs_region_end]["end"], + ) str_klifs, list_substring_idx = align_klifs_pocket_to_uniprot_seq( - idx_start = klifs_idx_start, - idx_end = klifs_idx_end, - str_uniprot = string_uniprot, - str_klifs = string_klifs, + idx_start=klifs_idx_start, + idx_end=klifs_idx_end, + str_uniprot=string_uniprot, + str_klifs=string_klifs, ) list_klifs_substr_actual.append(str_klifs) @@ -372,8 +318,8 @@ def iterate_klifs_alignment( # substring_idx = None if list_substring_idx is not None: - #TODO: analyze KLIFS PDB structures to determine contiguous regions - if (len(list_substring_idx) > 1): + # TODO: analyze KLIFS PDB structures to determine contiguous regions + if len(list_substring_idx) > 1: # if not last KLIFs region concatenate with susbequent regions if klifs_index + 1 < len(list_klifs): klifs_region_end = list_klifs[klifs_index + 1] @@ -383,16 +329,18 @@ def iterate_klifs_alignment( len_klifs = len(remove_gaps_from_klifs(str_klifs)) klifs_region_start = list_klifs[klifs_index - 1] klifs_idx_start = dict_klifs[klifs_region_start]["start"] - klifs_idx_start, klifs_idx_end = dict_klifs[klifs_region_start]["start"]-1, \ - dict_klifs[klifs_region_end]["end"] + klifs_idx_start, klifs_idx_end = ( + dict_klifs[klifs_region_start]["start"] - 1, + dict_klifs[klifs_region_end]["end"], + ) str_klifs, list_substring_idx = align_klifs_pocket_to_uniprot_seq( - idx_start = klifs_idx_start, - idx_end = klifs_idx_end, - str_uniprot = string_uniprot, - str_klifs = string_klifs, + idx_start=klifs_idx_start, + idx_end=klifs_idx_end, + str_uniprot=string_uniprot, + str_klifs=string_klifs, ) # if last KLIFS region offset by length of preceding KLIFS region with gaps removed - if (klifs_index + 1 == len(list_klifs) and len(list_substring_idx) != 0): + if klifs_index + 1 == len(list_klifs) and len(list_substring_idx) != 0: len_offset = len(remove_gaps_from_klifs(str_klifs)) - len_klifs list_substring_idx = [i + len_offset for i in list_substring_idx] @@ -412,10 +360,10 @@ def iterate_klifs_alignment( # substring_idx = np.nan dict_out = { - "list_klifs_region" : list_klifs_region, - "list_klifs_substr_actual" : list_klifs_substr_actual, - "list_klifs_substr_match" : list_klifs_substr_match, - "list_substring_idxs" : list_substring_idxs + "list_klifs_region": list_klifs_region, + "list_klifs_substr_actual": list_klifs_substr_actual, + "list_klifs_substr_match": list_klifs_substr_match, + "list_substring_idxs": list_substring_idxs, } return dict_out @@ -423,6 +371,7 @@ def iterate_klifs_alignment( class KLIFS(SwaggerAPIClient): """Class to interact with the KLIFS API.""" + def __init__(self): """Initialize KLIFS Class object. @@ -451,10 +400,10 @@ def query_api(self): klifs_api = SwaggerClient.from_url( self.url, config={ - "validate_requests": False, - "validate_responses": False, - "validate_swagger_spec": False - } + "validate_requests": False, + "validate_responses": False, + "validate_swagger_spec": False, + }, ) return klifs_api @@ -469,6 +418,7 @@ def get_klifs(self): class KinaseInfo(KLIFS): """Class to get information about a kinase from KLIFS.""" + def __init__( self, kinase_name: str, @@ -500,9 +450,7 @@ def __init__( self.species = species self._kinase_info = self.query_kinase_info() - def query_kinase_info( - self - ) -> dict[str, str | int | None]: + def query_kinase_info(self) -> dict[str, str | int | None]: """Get information about a kinase from KLIFS. Returns @@ -514,10 +462,10 @@ def query_kinase_info( try: kinase_info = ( self._klifs.Information.get_kinase_ID( - kinase_name=[self.kinase_name], - species=self.species) - .response() - .result[0] + kinase_name=[self.kinase_name], species=self.species + ) + .response() + .result[0] ) list_key = dir(kinase_info) @@ -539,9 +487,9 @@ def query_kinase_info( "pocket", "species", "subfamily", - "uniprot" - ] - dict_kinase_info = dict(zip(list_key, [None]*len(list_key))) + "uniprot", + ] + dict_kinase_info = dict(zip(list_key, [None] * len(list_key))) dict_kinase_info["name"] = self.kinase_name return dict_kinase_info diff --git a/src/missense_kinase_toolkit/databases/pfam.py b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/pfam.py similarity index 73% rename from src/missense_kinase_toolkit/databases/pfam.py rename to missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/pfam.py index 8bf44d1..f777fb2 100644 --- a/src/missense_kinase_toolkit/databases/pfam.py +++ b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/pfam.py @@ -7,6 +7,7 @@ class Pfam: """Class to interact with the Pfam API.""" + def __init__( self, uniprot_id: str, @@ -35,10 +36,7 @@ def query_pfam_api(self): url = f"{self.url}{self.uniprot_id}" header = {"Accept": "application/json"} - res = requests_wrapper.get_cached_session().get( - url, - headers=header - ) + res = requests_wrapper.get_cached_session().get(url, headers=header) if res.ok: if len(res.text) == 0: @@ -49,29 +47,44 @@ def query_pfam_api(self): # metadata for UniProt ID list_metadata = [entry["metadata"] for entry in list_json] - list_metadata = [{"pfam_accession" if k == "accession" else k:v for k,v in entry.items()} for entry in list_metadata] + list_metadata = [ + { + "pfam_accession" if k == "accession" else k: v + for k, v in entry.items() + } + for entry in list_metadata + ] # Pfam domains locations - list_locations = [entry["proteins"][0]["entry_protein_locations"][0]["fragments"][0] for entry in list_json] + list_locations = [ + entry["proteins"][0]["entry_protein_locations"][0]["fragments"][0] + for entry in list_json + ] # model information - list_model = [entry["proteins"][0]["entry_protein_locations"][0] for entry in list_json] + list_model = [ + entry["proteins"][0]["entry_protein_locations"][0] + for entry in list_json + ] [entry.pop("fragments", None) for entry in list_model] # protein information # do last because pop is an in-place operation list_protein = [entry["proteins"][0] for entry in list_json] [entry.pop("entry_protein_locations", None) for entry in list_protein] - list_protein = [{"uniprot" if k == "accession" else k:v for k,v in entry.items()} for entry in list_protein] + list_protein = [ + {"uniprot" if k == "accession" else k: v for k, v in entry.items()} + for entry in list_protein + ] df_concat = pd.concat( [ pd.DataFrame(list_protein), pd.DataFrame(list_metadata), pd.DataFrame(list_locations), - pd.DataFrame(list_model) + pd.DataFrame(list_model), ], - axis=1 + axis=1, ) return df_concat @@ -87,7 +100,7 @@ def find_pfam_domain( col_ref_id: str, col_ref_start: None | str = None, col_ref_end: None | str = None, - col_ref_domain : None | str = None, + col_ref_domain: None | str = None, ) -> str | None: """Find Pfam domain for a given HGNC symbol and position @@ -123,8 +136,13 @@ def find_pfam_domain( df_temp = df_ref.loc[df_ref[col_ref_id] == input_id].reset_index() try: - domain = df_temp.loc[((input_position >= df_temp[col_ref_start]) & - (input_position <= df_temp[col_ref_end])), col_ref_domain].values[0] + domain = df_temp.loc[ + ( + (input_position >= df_temp[col_ref_start]) + & (input_position <= df_temp[col_ref_end]) + ), + col_ref_domain, + ].values[0] return domain - except: + except IndexError: return None diff --git a/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/pkis2.py b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/pkis2.py new file mode 100644 index 0000000..88061fa --- /dev/null +++ b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/pkis2.py @@ -0,0 +1,55 @@ +import pandas as pd + +# drop values that cannot be matched to protein kinase sequence +LIST_DROP = [ + "PI3-KINASE-ALPHA", # lipid kinase + "PI3-KINASE-DELTA", # lipid kinase + "PI3-KINASE-GAMMA", # lipid kinase + "PI4-K-BETA", # lipid kinase + "SPHK1", # lipid kinase + "SPHK2", # lipid kinase + "AMP-A1B1G1", # B1G1 subunits not kinase entries + "AMP-A2B1G1", # B1G1 subunits not kinase entries + "CK2", # not sure if CSNK2A1 or CSNK2A2; catalog not available +] + +# dictionary of {string match : string replace} for exact matches +DICT_EXACT = { + "ARK5": "NUAK1", + "CK1": "CK1a", + "CRAF": "RAF1", + "LRRK": "LRRK2", + "MEK1": "MAP2K1", + "PAR-1B-ALPHA": "MARK2", + "PKC-BETA1": "PKC-B", + "PRAK": "MAPKAPK5", + "PTK5": "FRK", + "SNF1LK2": "QIK", +} + +# dictionary of {string match : string replace} for partial matches +DICT_PARTIAL = { + "AURORA": "AURK", + "ALPHA": "A", + "BETA": "B", + "DELTA": "D", + "EPSILON": "E", + "GAMMA": "G", + "-ETA": "H", + "IOTA": "I", + "THETA": "T", +} + + +def read_xlsx_file( + str_path: str = "../../../data/3. PKIS Nanosyn Assay Heatmaps.xlsx", + str_sheet: str = "Assay and Panel information", +) -> pd.DataFrame: + df = pd.read_excel(str_path, sheet_name=str_sheet) + return df + + +# def main(): +df_pkis2_km_atp = pd.read_csv("data/pkis2_km_atp.csv") + +# plot stacked barchart of PKIS2 ATP Km values where X-axis is the diff --git a/src/missense_kinase_toolkit/databases/requests_wrapper.py b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/requests_wrapper.py similarity index 100% rename from src/missense_kinase_toolkit/databases/requests_wrapper.py rename to missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/requests_wrapper.py index b14d2f7..6501654 100644 --- a/src/missense_kinase_toolkit/databases/requests_wrapper.py +++ b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/requests_wrapper.py @@ -1,8 +1,8 @@ -from requests_cache import CachedSession import os from functools import cache -from requests.adapters import HTTPAdapter, Retry +from requests.adapters import HTTPAdapter, Retry +from requests_cache import CachedSession # this script was written by Jeff Quinn (MSKCC, Tansey lab) REQUEST_CACHE_VAR = "REQUEST_CACHE" diff --git a/src/missense_kinase_toolkit/databases/scrapers.py b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/scrapers.py similarity index 71% rename from src/missense_kinase_toolkit/databases/scrapers.py rename to missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/scrapers.py index f1a4837..6e2b458 100644 --- a/src/missense_kinase_toolkit/databases/scrapers.py +++ b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/scrapers.py @@ -19,8 +19,9 @@ def kinhub( DataFrame of kinase information """ - from bs4 import BeautifulSoup import numpy as np + from bs4 import BeautifulSoup + # TODO: to fix ImportError # .venv/lib/python3.11/site-packages/janitor.py line 6 # "import ConfigParser" to "import configparser" @@ -30,24 +31,24 @@ def kinhub( page = requests_wrapper.get_cached_session().get(url) soup = BeautifulSoup(page.content, "html.parser") - list_header = [t for tr in soup.select('tr') for t in tr if t.name == 'th'] - dict_kinhub = {key.text.split('\n')[0]: [] for key in list_header} + list_header = [t for tr in soup.select("tr") for t in tr if t.name == "th"] + dict_kinhub = {key.text.split("\n")[0]: [] for key in list_header} - list_body = [t.text for tr in soup.select('tr') for t in tr if t.name == 'td'] + list_body = [t.text for tr in soup.select("tr") for t in tr if t.name == "td"] list_keys = list(dict_kinhub.keys()) mult = len(list_keys) i = 1 for entry in list_body: - if entry == '' or entry == 'nan': - dict_kinhub[list_keys[i-1]].append(np.nan) + if entry == "" or entry == "nan": + dict_kinhub[list_keys[i - 1]].append(np.nan) else: - dict_kinhub[list_keys[i-1]].append(entry) + dict_kinhub[list_keys[i - 1]].append(entry) if i % mult == 0: i = 1 else: - i +=1 + i += 1 df_kinhub = pd.DataFrame.from_dict(dict_kinhub) # df_kinhub = clean_names(df_kinhub) @@ -55,7 +56,11 @@ def kinhub( # aggregate rows with the same HGNC Name (e.g., multiple kinase domains like JAK) list_cols = df_kinhub.columns.to_list() list_cols.remove("HGNC Name") - df_kinhub_agg = df_kinhub.groupby(["HGNC Name"], as_index=False, sort=False).agg(set) - df_kinhub_agg[list_cols] = df_kinhub_agg[list_cols].map(lambda x : ', '.join(str(s) for s in x)) + df_kinhub_agg = df_kinhub.groupby(["HGNC Name"], as_index=False, sort=False).agg( + set + ) + df_kinhub_agg[list_cols] = df_kinhub_agg[list_cols].map( + lambda x: ", ".join(str(s) for s in x) + ) return df_kinhub_agg diff --git a/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/tests/__init__.py b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/tests/__init__.py new file mode 100644 index 0000000..e131175 --- /dev/null +++ b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/tests/__init__.py @@ -0,0 +1,3 @@ +""" +Empty init file in case you choose a package besides PyTest such as Nose which may look for such a file. +""" diff --git a/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/tests/test_databases.py b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/tests/test_databases.py new file mode 100644 index 0000000..5c40784 --- /dev/null +++ b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/tests/test_databases.py @@ -0,0 +1,313 @@ +import pytest + + +class TestDatabases: + def test_missense_kinase_toolkit_database_imported(self): + """Test if module is imported.""" + import sys + + import missense_kinase_toolkit.databases # noqa F401 + + assert "missense_kinase_toolkit.databases" in sys.modules + + def test_config(self): + from missense_kinase_toolkit.databases import config + + # test that the function to set the output directory works + with pytest.raises(SystemExit) as sample: + config.get_output_dir() + assert sample.type == SystemExit + assert sample.value.code == 1 + config.set_output_dir("test") + assert config.get_output_dir() == "test" + + # test that the function to set the request cache works + assert config.maybe_get_request_cache() is None + config.set_request_cache("test") + assert config.maybe_get_request_cache() == "test" + + # test that the function to set the cBioPortal instance works + with pytest.raises(SystemExit) as sample: + config.get_cbioportal_instance() + assert sample.type == SystemExit + assert sample.value.code == 1 + config.set_cbioportal_instance("test") + assert config.get_cbioportal_instance() == "test" + + # test that the function to set the cBioPortal token works + assert config.maybe_get_cbioportal_token() is None + config.set_cbioportal_token("test") + assert config.maybe_get_cbioportal_token() == "test" + + def test_io_utils(self): + import os + + import pandas as pd + + from missense_kinase_toolkit.databases import config, io_utils + + # os.environ["OUTPUT_DIR"] = "." + config.set_output_dir(".") + + # test that the functions to save and load dataframes work + df = pd.DataFrame({"A": [1, 2, 3], "B": [4, 5, 6]}) + io_utils.save_dataframe_to_csv(df, "test1.csv") + df_read = io_utils.load_csv_to_dataframe("test1.csv") + assert df.equals(df_read) + + # test that the function to concatenate csv files with glob works + io_utils.save_dataframe_to_csv(df, "test2.csv") + df_concat = io_utils.concatenate_csv_files_with_glob("*test*.csv") + assert df_concat.equals(pd.concat([df, df])) + + # remove the files created + os.remove("test1.csv") + os.remove("test2.csv") + + # test that the function to convert a string to a list works + assert io_utils.convert_str2list("a,b,c") == ["a", "b", "c"] + assert io_utils.convert_str2list("a, b, c") == ["a", "b", "c"] + + def test_requests_wrapper(self, capsys): + import requests + + from missense_kinase_toolkit.databases import uniprot, utils_requests + + uniprot.UniProt("TEST") + out, _ = capsys.readouterr() + assert out == "Error code: 400 (Bad request)\n" + + utils_requests.print_status_code_if_res_not_ok( + requests.get("https://rest.uniprot.org/uniprotkb/TEST"), + dict_status_code={400: "TEST"}, + ) + out, _ = capsys.readouterr() + assert out == "Error code: 400 (TEST)\n" + + utils_requests.print_status_code_if_res_not_ok( + requests.get("https://rest.uniprot.org/uniprotkb/TEST"), + dict_status_code={200: "TEST"}, + ) + out, _ = capsys.readouterr() + assert out == "Error code: 400\n" + + def test_cbioportal(self): + import os + + from missense_kinase_toolkit.databases import cbioportal, config + + config.set_cbioportal_instance("www.cbioportal.org") + config.set_output_dir(".") + + # test that the function to query the cBioPortal API works + cbioportal_instance = cbioportal.cBioPortal() + assert cbioportal_instance.get_instance() == "www.cbioportal.org" + assert ( + cbioportal_instance.get_url() + == "https://www.cbioportal.org/api/v2/api-docs" + ) + assert cbioportal_instance._cbioportal is not None + + # test that server status is up + assert ( + cbioportal_instance._cbioportal.Server_running_status.getServerStatusUsingGET() + .response() + .result["status"] + == "UP" + ) + + # test that Zehir cohort is available + study = "msk_impact_2017" + list_studies = ( + cbioportal_instance._cbioportal.Studies.getAllStudiesUsingGET().result() + ) + list_study_ids = [study.studyId for study in list_studies] + assert study in list_study_ids + + # test that the function to get all mutations by study works + df = cbioportal.Mutations(study).get_cbioportal_cohort_mutations() + assert df.shape[0] == 78142 + + # make sure save works + mutations_instance = cbioportal.Mutations(study) + mutations_instance.get_cbioportal_cohort_mutations(bool_save=True) + assert os.path.isfile(f"{mutations_instance.study_id}_mutations.csv") is True + os.remove(f"{mutations_instance.study_id}_mutations.csv") + + assert mutations_instance.get_study_id() == study + assert mutations_instance._mutations is not None + + def test_hgnc(self): + from missense_kinase_toolkit.databases import hgnc + + abl1 = hgnc.HGNC("Abl1", True) + abl1.maybe_get_symbol_from_hgnc_search() + assert abl1.hgnc == "ABL1" + assert ( + abl1.maybe_get_info_from_hgnc_fetch()["locus_type"][0] + == "gene with protein product" + ) + + abl1 = hgnc.HGNC("ENSG00000097007", False) + abl1.maybe_get_symbol_from_hgnc_search() + assert abl1.hgnc == "ABL1" + assert ( + abl1.maybe_get_info_from_hgnc_fetch()["locus_type"][0] + == "gene with protein product" + ) + + test = hgnc.HGNC("test", True) + test.maybe_get_symbol_from_hgnc_search() + assert test.ensembl is None + assert test.maybe_get_info_from_hgnc_fetch()["locus_type"] is None + + test = hgnc.HGNC("test", False) + test.maybe_get_symbol_from_hgnc_search() + assert test.hgnc is None + assert test.maybe_get_info_from_hgnc_fetch() is None + + test = hgnc.HGNC("temp") + test.maybe_get_symbol_from_hgnc_search( + custom_field="mane_select", custom_term="ENST00000318560.6" + ) + assert test.hgnc == "ABL1" + + def test_klifs(self): + from missense_kinase_toolkit.databases import klifs + + dict_egfr = klifs.KinaseInfo("EGFR")._kinase_info + + assert dict_egfr["family"] == "EGFR" + assert dict_egfr["full_name"] == "epidermal growth factor receptor" + assert dict_egfr["gene_name"] == "EGFR" + assert dict_egfr["group"] == "TK" + assert dict_egfr["iuphar"] == 1797 + assert dict_egfr["kinase_ID"] == 406 + assert dict_egfr["name"] == "EGFR" + assert ( + dict_egfr["pocket"] + == "KVLGSGAFGTVYKVAIKELEILDEAYVMASVDPHVCRLLGIQLITQLMPFGCLLDYVREYLEDRRLVHRDLAARNVLVITDFGLA" + ) + assert dict_egfr["species"] == "Human" + assert dict_egfr["uniprot"] == "P00533" + + def test_scrapers(self): + from missense_kinase_toolkit.databases import scrapers + + # test that the function to scrape the KinHub database works + df_kinhub = scrapers.kinhub() + assert df_kinhub.shape[0] == 517 + assert df_kinhub.shape[1] == 8 + assert "HGNC Name" in df_kinhub.columns + assert "UniprotID" in df_kinhub.columns + + def test_colors(self, capsys): + from missense_kinase_toolkit.databases import colors + + # correct mappings + assert colors.map_aa_to_single_letter_code("Ala") == "A" + assert colors.map_aa_to_single_letter_code("ALA") == "A" + assert colors.map_aa_to_single_letter_code("alanine") == "A" + assert colors.map_aa_to_single_letter_code("ALANINE") == "A" + assert colors.map_aa_to_single_letter_code("A") == "A" + assert colors.map_aa_to_single_letter_code("a") == "A" + + # incorrect mappings + TEST1 = "X" + assert colors.map_aa_to_single_letter_code(TEST1) is None + out, _ = capsys.readouterr() + assert out == f"Invalid single-letter amino acid: {TEST1.upper()}\n" + TEST2 = "AL" + assert colors.map_aa_to_single_letter_code(TEST2) is None + out, _ = capsys.readouterr() + assert out == f"Length error and invalid amino acid: {TEST2}\n" + TEST3 = "XYZ" + assert colors.map_aa_to_single_letter_code(TEST3) is None + out, _ = capsys.readouterr() + assert out == f"Invalid 3-letter amino acid: {TEST3.upper()}\n" + TEST4 = "TEST" + assert colors.map_aa_to_single_letter_code(TEST4) is None + out, _ = capsys.readouterr() + assert out == f"Invalid amino acid name: {TEST4.lower()}\n" + + # color mapping + DICT_COLORS = colors.DICT_COLORS + assert ( + colors.map_single_letter_aa_to_color( + "A", DICT_COLORS["ALPHABET_PROJECT"]["DICT_COLORS"] + ) + == "#F0A3FF" + ) + assert ( + colors.map_single_letter_aa_to_color( + "A", DICT_COLORS["ASAP"]["DICT_COLORS"] + ) + == "red" + ) + assert ( + colors.map_single_letter_aa_to_color( + "A", DICT_COLORS["RASMOL"]["DICT_COLORS"] + ) + == "#C8C8C8" + ) + assert ( + colors.map_single_letter_aa_to_color( + "A", DICT_COLORS["SHAPELY"]["DICT_COLORS"] + ) + == "#8CFF8C" + ) + assert ( + colors.map_single_letter_aa_to_color( + "A", DICT_COLORS["CLUSTALX"]["DICT_COLORS"] + ) + == "blue" + ) + assert ( + colors.map_single_letter_aa_to_color( + "A", DICT_COLORS["ZAPPO"]["DICT_COLORS"] + ) + == "#ffafaf" + ) + + def test_uniprot(self): + from missense_kinase_toolkit.databases import uniprot + + abl1 = uniprot.UniProt("P00519") + assert ( + abl1._sequence + == "MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASDGKLYVSSESRFNTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSISDEVEKELGKQGVRGAVSTLLQAPELPTKTRTSRRAAEHRDTTDVPEMPHSKGQGESDPLDHEPAVSPLLPRKERGPPEGGLNEDERLLPKDKKTNLFSALIKKKKKTAPTPPKRSSSFREMDGQPERRGAGEEEGRDISNGALAFTPLDTADPAKSPKPSNGAGVPNGALRESGGSGFRSPHLWKKSSTLTSSRLATGEEEGGGSSSKRFLRSCSASCVPHGAKDTEWRSVTLPRDLQSTGRQFDSSTFGGHKSEKPALPRKRAGENRSDQVTRGTVTPPPRLVKKNEEAADEVFKDIMESSPGSSPPNLTPKPLRRQVTVAPASGLPHKEEAGKGSALGTPAAAEPVTPTSKAGSGAPGGTSKGPAEESRVRRHKHSSESPGRDKGKLSRLKPAPPPPPAASAGKAGGKPSQSPSQEAAGEAVLGAKTKATSLVDAVNSDAAKPSQPGEGLKKPVLPATPKPQSAKPSGTPISPAPVPSTLPSASSALAGDQPSSTAFIPLISTRVSLRKTRQPPERIASGAITKGVVLDSTEALCLAISRNSEQMASHSAVLEAGKNLYTFCVSYVDSIQQMRNKFAFREAINKLENNLRELQICPATAGSGPAATQDFSKLLSSVKEISDIVQR" # noqa E501 + ) + + def test_pfam(self): + from missense_kinase_toolkit.databases import pfam + + # test that the function to find Pfam domain for a given HGNC symbol and position works + df_pfam = pfam.Pfam("P00519")._pfam + assert df_pfam.shape[0] == 4 + assert df_pfam.shape[1] == 18 + assert "uniprot" in df_pfam.columns + assert "start" in df_pfam.columns + assert "end" in df_pfam.columns + assert "name" in df_pfam.columns + assert ( + df_pfam.loc[ + df_pfam["name"] == "Protein tyrosine and serine/threonine kinase", + "start", + ].values[0] + == 242 + ) + assert ( + df_pfam.loc[ + df_pfam["name"] == "Protein tyrosine and serine/threonine kinase", "end" + ].values[0] + == 492 + ) + assert ( + pfam.find_pfam_domain( + input_id="p00519", + input_position=350, + df_ref=df_pfam, + col_ref_id="uniprot", + ) + == "Protein tyrosine and serine/threonine kinase" + ) diff --git a/src/missense_kinase_toolkit/databases/uniprot.py b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/uniprot.py similarity index 92% rename from src/missense_kinase_toolkit/databases/uniprot.py rename to missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/uniprot.py index ff0d43f..6db26ce 100644 --- a/src/missense_kinase_toolkit/databases/uniprot.py +++ b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/uniprot.py @@ -1,13 +1,12 @@ -import requests - from missense_kinase_toolkit.databases import requests_wrapper, utils_requests -class UniProt(): +class UniProt: """Class to interact with the UniProt API.""" + def __init__( - self, - uniprot_id: str, + self, + uniprot_id: str, ) -> None: """Initialize UniProt Class object. @@ -29,9 +28,9 @@ def __init__( self._sequence = self.get_uniprot_fasta() def get_uniprot_fasta( - self, - bool_seq : bool = True, - ) -> str | None: + self, + bool_seq: bool = True, + ) -> str | None: """Get FASTA sequence for UniProt ID. Parameters diff --git a/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/utils.py b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/utils.py new file mode 100644 index 0000000..7042502 --- /dev/null +++ b/missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/utils.py @@ -0,0 +1,176 @@ +from typing import Any + +import numpy as np + + +def try_except_split_concat_str( + str_in: str, + idx1: int, + idx2: int, + delim: str = "-", +) -> str: + """ + Split str_in on delim with exception handling. + + Parameters + ---------- + str_in : str + Input string + idx2 : int + Ending index + idx1 : int + Starting index + delim : str + Delimiter to split on + + Returns + ------- + str + Concatenated string containing the strings split on delim from idx1:idx2 + + """ + try: + str_out = ("").join( + [str_in.split(delim)[i].upper() for i in range(idx1, idx2 + 1)] + ) + return str_out + except (IndexError, AttributeError): + try: + str_out = str_in.split(delim)[0] + return str_out + except AttributeError: + str_out = str_in + return str_out + + +def create_strsplit_list( + list_in: list[str], + idx_start: int = 0, + idx_end: int = 2, +) -> list[str]: + """ + Split list or Series of strings on delim with exception handling. + + """ + return [ + [ + try_except_split_concat_str(x, idx_start, i) + for i in range(idx_start, idx_end + 1) + ] + for x in list_in + ] + + +def try_except_match_str2dict( + str_in: str, + dict_in: dict[str, Any], + bool_keyout: bool = True, +) -> Any: + """ + Dictionary match with exception handling. + + Parameters + ---------- + str_in : str + Input string + dict_in : dict[str, Any] + Dictionary where keys are strings to match with str_in + bool_keyout : bool + If true and no match, return string + + Returns + ------- + Any + Returns either dictionary value if match, str_in if no match and bool_keyout = True else None + + """ + try: + return dict_in[str_in] + except KeyError: + if bool_keyout: + return str_in + else: + None + + +def return_list_match_indices( + str_in: str, + list_in: list[str | list[str]], +) -> list[int] | list | None: + """ + Return list of indices where str_in matches entry or entries in list_in. + + Parameters + ---------- + str_in : str + Input string to check for matches in list_in + list_in : list[str | list[str]] + List of string or list of list of strings to check for str_in match + + Returns + ------- + list[int] | None + Returns index of matching entries in list + + """ + if type(list_in[0]) is str: + list_out = [idx for idx, hgnc in enumerate(list_in) if hgnc.upper() in str_in] + return list_out + elif type(list_in[0]) is list: + list_out = [ + idx + for idx, list_nest in enumerate(list_in) + for hgnc in list_nest + if hgnc.upper() in str_in + ] + return list_out + else: + print(f"Input type of {type(list_in[0])} cannot be handled.") + + +def replace_string_using_dict( + str_in: str, + dict_in: dict[str, str], +) -> str: + """ + Replace any partial matches in a string using a dictionary of {string match : string replace}. + + Parameters + ---------- + str_in : str + Input string to replace partial matches + dict_in : dict[str, str] + Dictionary of {string match : string replace} + + Returns + ------- + str_out : str + String with any partial matches replaced + + """ + str_out = str_in + try: + for key, val in dict_in.items(): + str_out = str_out.upper().replace(key, val) + return str_out + except AttributeError: + return str_out + + +def return_list_out( + list_kinhub_uniprot: list[str | float], + list_assay_name: list[str], +): + list_out = [ + return_list_match_indices(x, list_kinhub_uniprot) for x in list_assay_name + ] + set_out = [set(i) if i is not np.nan else np.nan for i in list_out] + list_out = [i[0] if len(j) != 0 else np.nan for i, j in zip(list_out, set_out)] + return list_out, set_out + + +def try_except_convert_str2int(str_in: str): + try: + return int(str_in) + except ValueError: + return str_in diff --git 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-[package.extras] -docs = ["Sphinx", "repoze.sphinx.autointerface", "sphinx-rtd-theme"] -test = ["coverage (>=5.0.3)", "zope.event", "zope.testing"] -testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"] - -[metadata] -lock-version = "2.0" -python-versions = "^3.9" -content-hash = "64e2993ed648621a0813b9ad50f35feb45b0f6201fe3633f7f1455c7f0c144c2" diff --git a/pyproject.toml b/pyproject.toml index a1bab0b..9eb78a2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,73 +1,5 @@ -[tool.poetry] -name = "missense-kinase-toolkit" -# https://github.com/mtkennerly/poetry-dynamic-versioning/issues/14 -# https://browniebroke.com/blog/convert-existing-poetry-to-src-layout/ -version = "0.0.0.dev42+ga57ba38" -description = "An ETL pipeline package to facilitate structure-based ML for human kinase property prediction" -authors = ["Jess White "] -license = "MIT" -readme = "README.md" -repository = "https://github.com/choderalab/missense_kinase_toolkit/" -classifiers = [ - "License :: OSI Approved :: MIT License", - "Programming Language :: Python :: 3", -] -#https://safjan.com/the-importance-of-adding-py-typed-file-to-your-typed-package/ -packages = [ - {include = "missense_kinase_toolkit", from = "src"}, - {include = "missense_kinase_toolkit/py.typed", from = "src"} -] - -[tool.poetry.dependencies] -python = "^3.9" -setuptools = "^70.0.0" -pydantic = "^2.7.4" -tqdm = "4.66.3" -pandas = ">=2,<3" -requests = ">=2.28.1,<3" -requests-cache = ">=0.9.7,<1" -bravado = "^11.0.3" -janitor = "^0.1.1" -beautifulsoup4 = "^4.12.3" -ipykernel = "^6.29.4" -jupyter = "^1.0.0" -biopython = "^1.83" -bokeh = "^3.4.1" -seaborn = "^0.13.2" -scipy = "^1.13.1" - -[tool.poetry.group.dev.dependencies] -black = "^24.3.0" -flake8 = "^7.0.0" -sphinx = "^7.3.7" -sphinx-rtd-theme = "^2.0.0" - -[tool.poetry.group.test.dependencies] -pytest = "^8.0.1" -pytest-runner = "^6.0.1" - -# https://stackoverflow.com/questions/60971502/python-poetry-how-to-install-optional-dependencies -# [tool.poetry.extras] -# notebooks = ["jupyter", "ipykernel"] - -[tool.pytest.ini_options] -pythonpath = ["src"] - -[tool.poetry.scripts] -extract_cbioportal = "missense_kinase_toolkit.databases.cli.extract_cbioportal:main" -transform_cbioportal = "missense_kinase_toolkit.databases.cli.transform_cbioportal:main" - -[tool.poetry-dynamic-versioning] -enable = false -vcs = "git" -pattern = "^(?P\\d+\\.\\d+\\.\\d+)(-?((?P[a-zA-Z]+)\\.?(?P\\d+)?))?" -format-jinja = """ - {%- if distance == 0 -%} - {{- base -}} - {%- else -%} - {{- base }}.dev{{ distance }}+g{{commit}} - {%- endif -%} -""" -[build-system] -requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"] -build-backend = "poetry_dynamic_versioning.backend" +[tool.flake8] +max-line-length = 88 +extend-ignore = ['E203','E501'] +[tool.isort] +profile = "black" diff --git a/setup.cfg b/setup.cfg index ed77953..f263bed 100644 --- a/setup.cfg +++ b/setup.cfg @@ -5,18 +5,12 @@ omit = # Omit the tests */tests/* - # Omit generated versioneer - missense_kinase_toolkit/_version.py [yapf] # YAPF, in .style.yapf files this shows up as "[style]" header -COLUMN_LIMIT = 119 +COLUMN_LIMIT = 88 INDENT_WIDTH = 4 USE_TABS = False -[flake8] -# Flake8, PyFlakes, etc -max-line-length = 119 - [aliases] test = pytest diff --git a/src/README.md b/src/README.md deleted file mode 100644 index f9bf1ab..0000000 --- a/src/README.md +++ /dev/null @@ -1 +0,0 @@ -#TODO diff --git a/src/__init__.py b/src/__init__.py deleted file mode 100644 index 091ac24..0000000 --- a/src/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -"""An ETL pipeline package to facilitate structure-based ML for missense human kinase property prediction""" - -from missense_kinase_toolkit import * diff --git a/src/missense_kinase_toolkit/__init__.py b/src/missense_kinase_toolkit/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/src/missense_kinase_toolkit/databases/cli/__init__.py b/src/missense_kinase_toolkit/databases/cli/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/src/missense_kinase_toolkit/databases/cli/extract_cbioportal.py b/src/missense_kinase_toolkit/databases/cli/extract_cbioportal.py deleted file mode 100755 index 373fc34..0000000 --- a/src/missense_kinase_toolkit/databases/cli/extract_cbioportal.py +++ /dev/null @@ -1,65 +0,0 @@ -#!/usr/bin/env python - -import argparse - -from missense_kinase_toolkit.databases import config, io_utils, cbioportal - -def parsearg_utils(): - parser = argparse.ArgumentParser( - description="Get mutations from cBioPortal instance for all specified studies." - ) - - parser.add_argument( - "--outDir", - type=str, - help="Required: Output directory path (str)", - ) - - parser.add_argument( - "--requestsCache", - type=str, - default="requests_cache", - help="Optional: Requests cache; default: `requests_cache` (str)", - ) - - parser.add_argument( - "--cohort", - type=str, - help="Optional: cBioPortal cohort IDs separated by commas (e.g., `msk_impact_2017` for Zehir, 2017 and `mskimpact` for MSKCC clinical sequencing cohort) (str)", - default="msk_impact_2017", - ) - - parser.add_argument( - "--instance", - type=str, - help="Optional: cBioPortal instance (e.g., `cbioportal.mskcc.org`). Default: `www.cbioportal.org` (str)", - default="www.cbioportal.org", - ) - - parser.add_argument( - "--token", - type=str, - default="", - help="Optional: cBioPortal API token (str)", - ) - - # TODO: add logging functionality - return parser - - -def main(): - args = parsearg_utils().parse_args() - - list_studies = io_utils.convert_str2list(args.cohort) - - config.set_output_dir(args.outDir) - config.set_cbioportal_instance(args.instance) - - try: - if args.token != "": - config.set_cbioportal_token(args.token) - except AttributeError: - pass - - for study in list_studies: - cbioportal.Mutations(study).get_cbioportal_cohort_mutations(bool_save=True) diff --git a/src/missense_kinase_toolkit/databases/cli/extract_kinase_annotations.py b/src/missense_kinase_toolkit/databases/cli/extract_kinase_annotations.py deleted file mode 100755 index c34895d..0000000 --- a/src/missense_kinase_toolkit/databases/cli/extract_kinase_annotations.py +++ /dev/null @@ -1,62 +0,0 @@ -#!/usr/bin/env python - -import argparse - -import pandas as pd - -from missense_kinase_toolkit.databases import config, io_utils, scrapers, klifs - -def parsearg_utils(): - parser = argparse.ArgumentParser( - description="Get kinase annotations from KinHub and KLIFS databases." - ) - - parser.add_argument( - "--outDir", - type=str, - help="Required: Output directory path (str)", - ) - - parser.add_argument( - "--requestsCache", - type=str, - default="requests_cache", - help="Optional: Requests cache; default: `requests_cache` (str)", - ) - - parser.add_argument( - "--csvKinhub", - type=str, - default="kinhub.csv", - help="Optional: CSV file in outDir that contains Kinhub kinase info; default: `kinhub.csv` (str)", - ) - - parser.add_argument( - "--csvKLIFS", - type=str, - default="klifs.csv", - help="Optional: CSV file in outDir that contains KLIFS kinase info; default: `klifs.csv` (str)", - ) - - # TODO: add logging functionality - return parser - - -def main(): - args = parsearg_utils().parse_args() - - config.set_output_dir(args.outDir) - config.set_request_cache(args.requestsCache) - - # get KinHub list of kinases - df_kinhub = scrapers.kinhub() - io_utils.save_dataframe_to_csv(df_kinhub, args.csvKinhub) - - # get KLIFS annotations - list_kinase_hgnc = df_kinhub["HGNC Name"].to_list() - dict_kinase_info = {} - for kinase in list_kinase_hgnc: - dict_kinase_info[kinase] = klifs.KinaseInfo(kinase)._kinase_info - df_klifs = pd.DataFrame(dict_kinase_info).T - df_klifs = df_klifs.rename_axis("HGNC Name").reset_index() - io_utils.save_dataframe_to_csv(df_klifs, args.csvKLIFS) diff --git a/src/missense_kinase_toolkit/databases/cli/transform_cbioportal.py b/src/missense_kinase_toolkit/databases/cli/transform_cbioportal.py deleted file mode 100755 index 096d0a9..0000000 --- a/src/missense_kinase_toolkit/databases/cli/transform_cbioportal.py +++ /dev/null @@ -1,79 +0,0 @@ -#!/usr/bin/env python - -import argparse - -from missense_kinase_toolkit.databases import config, io_utils - - -def parsearg_utils(): - parser = argparse.ArgumentParser( - description="Concatenate, remove duplicates, and extract genes and mutation types of interest from cBioPortal data." - ) - - parser.add_argument( - "--mutationTypes", - type=str, - help="Optional: Mutation type(s) to extract, separated by commas; default: `Missense_Mutation` (str)", - default="Missense_Mutation", - ) - - parser.add_argument( - "--outDir", - type=str, - help="Required: Output directory path (str)", - ) - - parser.add_argument( - "--requestsCache", - type=str, - default="requests_cache", - help="Optional: Requests cache; default: requests_cache (str)", - ) - - parser.add_argument( - "--listCols", - type=str, - default="HGNC Name, UniprotID", - help="Optional: List of columns to merge separated by comma with the first as the merge on column of HGNC gene names; default: `HGNC Name, UniprotID` (str)", - ) - - parser.add_argument( - "--csvRef", - type=str, - default="kinhub.csv", - help="Optional: CSV file in outDir that contains; default: `kinhub.csv` (str)", - ) - - # TODO: add logging functionality - return parser - - -def main(): - args = parsearg_utils().parse_args() - - config.set_output_dir(args.outDir) - config.set_request_cache(args.requestsCache) - - list_mutations = io_utils.convert_str2list(args.mutationTypes) - list_cols = io_utils.convert_str2list(args.listCols) - - df_cbioportal = io_utils.concatenate_csv_files_with_glob("*_mutations.csv") - - df_kinhub = io_utils.load_csv_to_dataframe(args.csvRef) - # df_kinhub = scrapers.kinhub() - # io_utils.save_dataframe_to_csv(df_kinhub, "kinhub.csv") - - list_kinase_hgnc = df_kinhub[list_cols[0]].to_list() - # list_kinase_hgnc = df_kinhub["HGNC Name"].to_list() - - df_subset = df_cbioportal.loc[df_cbioportal["mutationType"].isin(list_mutations), ].reset_index(drop=True) - df_subset = df_subset.loc[df_subset["hugoGeneSymbol"].isin(list_kinase_hgnc), ].reset_index(drop=True) - - # list_cols = ["HGNC Name", "UniprotID"] - df_subset_merge = df_subset.merge(df_kinhub[list_cols], - how = "left", - left_on = "hugoGeneSymbol", - right_on = list_cols[0]) - df_subset_merge = df_subset_merge.drop([list_cols[0]], axis=1) - - io_utils.save_dataframe_to_csv(df_subset_merge, "transformed_mutations.csv") diff --git a/src/nextflow/README.MD b/src/nextflow/README.MD deleted file mode 100644 index c95c83d..0000000 --- a/src/nextflow/README.MD +++ /dev/null @@ -1,24 +0,0 @@ -# NextFlow workflow to run pipeline - -To run: `nextflow run main.nf -params-file params.json` - -Generate own `params.json` file using the following parameters: -``` -{ - "CBIOPORTAL_COHORT" : "TODO", - "OUTPUT_DIR" : "TODO", - "CBIOPORTAL_INSTANCE" : "TODO", - "CBIOPORTAL_TOKEN" : "TODO", - "REQUESTS_CACHE" : "TODO" -} -``` - -Below is a description of what each variable should contain. If variable is optional and not in use, do not create any entry in the `json` file. - -| Variable | Optional | Description | -| :--------------------| :------: | :----------------------------------------- | -| CBIOPORTAL_COHORT | No | cBioPortal cohort to analyze | -| OUTPUT_DIR | No | Path to outdir to save data | -| CBIOPORTAL_INSTANCE | Yes | `cbioportal.org` if none provided | -| CBIOPORTAL_TOKEN | Yes | Data Access Token if using private instance| -| REQUESTS_CACHE | Yes | Boolean of whether to cache requests data | diff --git a/src/nextflow/extract_cbioportal.nf b/src/nextflow/extract_cbioportal.nf deleted file mode 100644 index b9462ca..0000000 --- a/src/nextflow/extract_cbioportal.nf +++ /dev/null @@ -1,16 +0,0 @@ -process PROCESS_CBIOPORTAL { - input: - tuple val(cbio_cohort), path(out_dir), val(cbio_inst), val(cbio_token), path(request_cache) - - output: - path("${out_dir}/cbioportal") - """ - export PYTHONHASHSEED=0 - process_cbioportal \ - --cohort ${cbio_cohort} \ - --outDir ${out_dir} \ - --instance ${cbio_inst} \ - --token ${cbio_token} \ - --requestsCache ${request_cache} - """ -} diff --git a/src/nextflow/modules/extract_cbioportal.nf b/src/nextflow/modules/extract_cbioportal.nf deleted file mode 100644 index b9462ca..0000000 --- a/src/nextflow/modules/extract_cbioportal.nf +++ /dev/null @@ -1,16 +0,0 @@ -process PROCESS_CBIOPORTAL { - input: - tuple val(cbio_cohort), path(out_dir), val(cbio_inst), val(cbio_token), path(request_cache) - - output: - path("${out_dir}/cbioportal") - """ - export PYTHONHASHSEED=0 - process_cbioportal \ - --cohort ${cbio_cohort} \ - --outDir ${out_dir} \ - --instance ${cbio_inst} \ - --token ${cbio_token} \ - --requestsCache ${request_cache} - """ -} diff --git a/src/nextflow/nextflow.config b/src/nextflow/nextflow.config deleted file mode 100644 index 78f477f..0000000 --- a/src/nextflow/nextflow.config +++ /dev/null @@ -1,27 +0,0 @@ -profiles { - conda { - conda.enabled = true - } - mamba { - conda.enabled = true - conda.useMamba = true - } - micromamba { - conda.enabled = true - conda.useMicromamba = true - } - juno { - // singularity { - // enabled = true - // autoMounts = true - // } - process { - executor = 'lsf' - } - executor { - name = 'lsf' - perJobMemLimit = true - queueSize = 25 - } - } -} diff --git a/src/nextflow/process_cbioportal.nf b/src/nextflow/process_cbioportal.nf deleted file mode 100644 index 5625530..0000000 --- a/src/nextflow/process_cbioportal.nf +++ /dev/null @@ -1,24 +0,0 @@ -process PROCESS_CBIOPORTAL { - // tag "$meta.id" - // label 'process_medium' - // container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - // 'docker://jeffquinnmsk/pan_preclinical_etl:latest' : - // 'docker.io/jeffquinnmsk/pan_preclinical_etl:latest' }" - - input: - tuple val(meta), path(raw_data), path(studies), path(source_files), path(request_cache), val(study_name) - - output: - tuple val(meta), path("${prefix}/per_study_results/${study_name}"), emit: etl_results - - """ - export PYTHONHASHSEED=0 - mkdir -p "${prefix}/per_study_results/${study_name}" - process_cbioportal \ - --data-dir ${raw_data} \ - --output-dir ${prefix}/per_study_results/${study_name} \ - --studies ${studies} \ - --source-files ${source_files} \ - --study-id ${study_name} - """ -} diff --git a/tests/test_databases.py b/tests/test_databases.py deleted file mode 100644 index 0d8855f..0000000 --- a/tests/test_databases.py +++ /dev/null @@ -1,257 +0,0 @@ -""" -Unit and regression test for the missense_kinase_toolkit package. -""" - -# Import package, test suite, and other packages as needed -import pytest - - -def test_missense_kinase_toolkit_database_imported(): - """Test if module is imported.""" - import sys - import missense_kinase_toolkit.databases - - assert "missense_kinase_toolkit.databases" in sys.modules - - -def test_config(): - from missense_kinase_toolkit.databases import config - - # test that the function to set the output directory works - with pytest.raises(SystemExit) as sample: - config.get_output_dir() - assert sample.type == SystemExit - assert sample.value.code == 1 - config.set_output_dir("test") - assert config.get_output_dir() == "test" - - # test that the function to set the request cache works - assert config.maybe_get_request_cache() is None - config.set_request_cache("test") - assert config.maybe_get_request_cache() == "test" - - # test that the function to set the cBioPortal instance works - with pytest.raises(SystemExit) as sample: - config.get_cbioportal_instance() - assert sample.type == SystemExit - assert sample.value.code == 1 - config.set_cbioportal_instance("test") - assert config.get_cbioportal_instance() == "test" - - # test that the function to set the cBioPortal token works - assert config.maybe_get_cbioportal_token() is None - config.set_cbioportal_token("test") - assert config.maybe_get_cbioportal_token() == "test" - - -def test_io_utils(): - import pandas as pd - import os - from missense_kinase_toolkit.databases import io_utils, config - - # os.environ["OUTPUT_DIR"] = "." - config.set_output_dir(".") - - # test that the functions to save and load dataframes work - df = pd.DataFrame({"A": [1, 2, 3], "B": [4, 5, 6]}) - io_utils.save_dataframe_to_csv(df, "test1.csv") - df_read = io_utils.load_csv_to_dataframe("test1.csv") - assert df.equals(df_read) - - # test that the function to concatenate csv files with glob works - io_utils.save_dataframe_to_csv(df, "test2.csv") - df_concat = io_utils.concatenate_csv_files_with_glob("*test*.csv") - assert df_concat.equals(pd.concat([df, df])) - - # remove the files created - os.remove("test1.csv") - os.remove("test2.csv") - - # test that the function to convert a string to a list works - assert io_utils.convert_str2list("a,b,c") == ["a", "b", "c"] - assert io_utils.convert_str2list("a, b, c") == ["a", "b", "c"] - - -def test_requests_wrapper(capsys): - import requests - from missense_kinase_toolkit.databases import uniprot, utils_requests - - uniprot.UniProt("TEST") - out, _ = capsys.readouterr() - assert out == "Error code: 400 (Bad request)\n" - - utils_requests.print_status_code_if_res_not_ok( - requests.get("https://rest.uniprot.org/uniprotkb/TEST"), - dict_status_code = {400: "TEST"} - ) - out, _ = capsys.readouterr() - assert out == "Error code: 400 (TEST)\n" - - utils_requests.print_status_code_if_res_not_ok( - requests.get("https://rest.uniprot.org/uniprotkb/TEST"), - dict_status_code = {200: "TEST"} - ) - out, _ = capsys.readouterr() - assert out == "Error code: 400\n" - - -def test_cbioportal(): - import os - from missense_kinase_toolkit.databases import config, cbioportal - - config.set_cbioportal_instance("www.cbioportal.org") - config.set_output_dir(".") - - # test that the function to query the cBioPortal API works - cbioportal_instance = cbioportal.cBioPortal() - assert cbioportal_instance.get_instance() == "www.cbioportal.org" - assert cbioportal_instance.get_url() == "https://www.cbioportal.org/api/v2/api-docs" - assert cbioportal_instance._cbioportal is not None - - # test that server status is up - assert cbioportal_instance._cbioportal.Server_running_status.getServerStatusUsingGET().response().result["status"] == "UP" - - # test that Zehir cohort is available - study = "msk_impact_2017" - list_studies = cbioportal_instance._cbioportal.Studies.getAllStudiesUsingGET().result() - list_study_ids = [study.studyId for study in list_studies] - assert study in list_study_ids - - # test that the function to get all mutations by study works - df = cbioportal.Mutations(study).get_cbioportal_cohort_mutations() - assert df.shape[0] == 78142 - - # make sure save works - mutations_instance = cbioportal.Mutations(study) - mutations_instance.get_cbioportal_cohort_mutations(bool_save=True) - assert os.path.isfile(f"{mutations_instance.study_id}_mutations.csv") == True - os.remove(f"{mutations_instance.study_id}_mutations.csv") - - assert mutations_instance.get_study_id() == study - assert mutations_instance._mutations is not None - - -def test_hgnc(): - from missense_kinase_toolkit.databases import hgnc - - abl1 = hgnc.HGNC("Abl1", True) - abl1.maybe_get_symbol_from_hgnc_search() - assert abl1.hgnc == "ABL1" - assert abl1.maybe_get_info_from_hgnc_fetch()["locus_type"][0] == "gene with protein product" - - abl1 = hgnc.HGNC("ENSG00000097007", False) - abl1.maybe_get_symbol_from_hgnc_search() - assert abl1.hgnc == "ABL1" - assert abl1.maybe_get_info_from_hgnc_fetch()["locus_type"][0] == "gene with protein product" - - test = hgnc.HGNC("test", True) - test.maybe_get_symbol_from_hgnc_search() - assert test.ensembl is None - assert test.maybe_get_info_from_hgnc_fetch()["locus_type"] is None - - test = hgnc.HGNC("test", False) - test.maybe_get_symbol_from_hgnc_search() - assert test.hgnc is None - assert test.maybe_get_info_from_hgnc_fetch() is None - - test = hgnc.HGNC("temp") - test.maybe_get_symbol_from_hgnc_search( - custom_field="mane_select", - custom_term="ENST00000318560.6" - ) - assert test.hgnc == "ABL1" - - -def test_klifs(): - from missense_kinase_toolkit.databases import klifs - - dict_egfr = klifs.KinaseInfo("EGFR")._kinase_info - - assert dict_egfr["family"] == "EGFR" - assert dict_egfr["full_name"] == "epidermal growth factor receptor" - assert dict_egfr["gene_name"] == "EGFR" - assert dict_egfr["group"] == "TK" - assert dict_egfr["iuphar"] == 1797 - assert dict_egfr["kinase_ID"] == 406 - assert dict_egfr["name"] == "EGFR" - assert dict_egfr["pocket"] == "KVLGSGAFGTVYKVAIKELEILDEAYVMASVDPHVCRLLGIQLITQLMPFGCLLDYVREYLEDRRLVHRDLAARNVLVITDFGLA" - assert dict_egfr["species"] == "Human" - assert dict_egfr["uniprot"] == "P00533" - - -def test_scrapers(): - from missense_kinase_toolkit.databases import scrapers - - # test that the function to scrape the KinHub database works - df_kinhub = scrapers.kinhub() - assert df_kinhub.shape[0] == 517 - assert df_kinhub.shape[1] == 8 - assert "HGNC Name" in df_kinhub.columns - assert "UniprotID" in df_kinhub.columns - - -def test_colors(capsys): - from missense_kinase_toolkit.databases import colors - - # correct mappings - assert colors.map_aa_to_single_letter_code("Ala") == "A" - assert colors.map_aa_to_single_letter_code("ALA") == "A" - assert colors.map_aa_to_single_letter_code("alanine") == "A" - assert colors.map_aa_to_single_letter_code("ALANINE") == "A" - assert colors.map_aa_to_single_letter_code("A") == "A" - assert colors.map_aa_to_single_letter_code("a") == "A" - - # incorrect mappings - TEST1 = "X" - assert colors.map_aa_to_single_letter_code(TEST1) is None - out, _ = capsys.readouterr() - assert out == f"Invalid single-letter amino acid: {TEST1.upper()}\n" - TEST2 = "AL" - assert colors.map_aa_to_single_letter_code(TEST2) is None - out, _ = capsys.readouterr() - assert out == f"Length error and invalid amino acid: {TEST2}\n" - TEST3 = "XYZ" - assert colors.map_aa_to_single_letter_code(TEST3) is None - out, _ = capsys.readouterr() - assert out == f"Invalid 3-letter amino acid: {TEST3.upper()}\n" - TEST4 = "TEST" - assert colors.map_aa_to_single_letter_code(TEST4) is None - out, _ = capsys.readouterr() - assert out == f"Invalid amino acid name: {TEST4.lower()}\n" - - # color mapping - DICT_COLORS = colors.DICT_COLORS - assert colors.map_single_letter_aa_to_color("A", DICT_COLORS["ALPHABET_PROJECT"]["DICT_COLORS"]) == "#F0A3FF" - assert colors.map_single_letter_aa_to_color("A", DICT_COLORS["ASAP"]["DICT_COLORS"]) == "red" - assert colors.map_single_letter_aa_to_color("A", DICT_COLORS["RASMOL"]["DICT_COLORS"]) == "#C8C8C8" - assert colors.map_single_letter_aa_to_color("A", DICT_COLORS["SHAPELY"]["DICT_COLORS"]) == "#8CFF8C" - assert colors.map_single_letter_aa_to_color("A", DICT_COLORS["CLUSTALX"]["DICT_COLORS"]) == "blue" - assert colors.map_single_letter_aa_to_color("A", DICT_COLORS["ZAPPO"]["DICT_COLORS"]) == "#ffafaf" - - -def test_uniprot(): - from missense_kinase_toolkit.databases import uniprot - - abl1 = uniprot.UniProt("P00519") - assert abl1._sequence == "MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASDGKLYVSSESRFNTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSISDEVEKELGKQGVRGAVSTLLQAPELPTKTRTSRRAAEHRDTTDVPEMPHSKGQGESDPLDHEPAVSPLLPRKERGPPEGGLNEDERLLPKDKKTNLFSALIKKKKKTAPTPPKRSSSFREMDGQPERRGAGEEEGRDISNGALAFTPLDTADPAKSPKPSNGAGVPNGALRESGGSGFRSPHLWKKSSTLTSSRLATGEEEGGGSSSKRFLRSCSASCVPHGAKDTEWRSVTLPRDLQSTGRQFDSSTFGGHKSEKPALPRKRAGENRSDQVTRGTVTPPPRLVKKNEEAADEVFKDIMESSPGSSPPNLTPKPLRRQVTVAPASGLPHKEEAGKGSALGTPAAAEPVTPTSKAGSGAPGGTSKGPAEESRVRRHKHSSESPGRDKGKLSRLKPAPPPPPAASAGKAGGKPSQSPSQEAAGEAVLGAKTKATSLVDAVNSDAAKPSQPGEGLKKPVLPATPKPQSAKPSGTPISPAPVPSTLPSASSALAGDQPSSTAFIPLISTRVSLRKTRQPPERIASGAITKGVVLDSTEALCLAISRNSEQMASHSAVLEAGKNLYTFCVSYVDSIQQMRNKFAFREAINKLENNLRELQICPATAGSGPAATQDFSKLLSSVKEISDIVQR" - - -def test_pfam(): - from missense_kinase_toolkit.databases import pfam - - # test that the function to find Pfam domain for a given HGNC symbol and position works - df_pfam = pfam.Pfam("P00519")._pfam - assert df_pfam.shape[0] == 4 - assert df_pfam.shape[1] == 18 - assert "uniprot" in df_pfam.columns - assert "start" in df_pfam.columns - assert "end" in df_pfam.columns - assert "name" in df_pfam.columns - assert df_pfam.loc[df_pfam["name"] == "Protein tyrosine and serine/threonine kinase", "start"].values[0] == 242 - assert df_pfam.loc[df_pfam["name"] == "Protein tyrosine and serine/threonine kinase", "end"].values[0] == 492 - assert pfam.find_pfam_domain( - input_id="p00519", - input_position=350, - df_ref=df_pfam, - col_ref_id="uniprot" - ) == "Protein tyrosine and serine/threonine kinase"