diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..62e6727 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,47 @@ +# using ubuntu LTS version +# from https://luis-sena.medium.com/creating-the-perfect-python-dockerfile-51bdec41f1c8 + +# using ubuntu LTS version +FROM ubuntu:20.04 + +RUN apt-get update && apt-get install --no-install-recommends -y python3.8-dev \ + python3.8-venv python3-pip python3-wheel build-essential && \ + apt-get clean && rm -rf /var/lib/apt/lists/* + +# create and activate virtual environment +RUN python3.8 -m venv /opt/venv +ENV PATH="/opt/venv/bin:$PATH" + +# Install Poetry +RUN python3 -m pip install pipx && \ + python3 -m pipx ensurepath && \ + pipx install poetry && \ + pipx ensurepath + +# Set up environment variables for Poetry +ENV PATH="$PATH:/root/.local/bin" +ENV POETRY_HOME="/root/.poetry" + +# export path +ENV PATH="$PATH:/root/.local/share/pipx/venvs/poetry/bin/" + +# Install Pandas and Keras in a virtual environment using Poetry +WORKDIR /app + +# Copy only the pyproject.toml and poetry.lock files initially to leverage Docker cache +COPY pyproject.toml ./ + +# upgrade pip +RUN pip install --upgrade pip setuptools wheel + +# Install dependencies +#RUN poetry install --no-root -vvv + +# Copy the rest of the application code +COPY . . + +# append Python module dir to Path +RUN PATH="${PATH}:/app/modules" + +# Set the default command to run the application +CMD ["python", "framepool_annotate.py"] diff --git a/framepool_annotate.py b/framepool_annotate.py new file mode 100644 index 0000000..3d8c30d --- /dev/null +++ b/framepool_annotate.py @@ -0,0 +1,42 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +""" +Created on Wed Feb 8 07:26:34 2023 + +Script to invoke FramePool annotation provided an input dataframe path + +@author: bbowles +""" + +import sys +sys.path.append('/app/modules/') +from kipoi_functions import framepool_caller + +def main(): + # Create an argument parser + parser = argparse.ArgumentParser(description="Annotate an ORFA file with FramePool ribosome load prediction.") + + # Add the "--input" argument + parser.add_argument("--input", help="Input, tab-delimited ORFA file.", required=True) + + # Parse the command line arguments + args = parser.parse_args() + + # Get and print the full path + path = args.input + + if path.endswith(".tsv"): + + # run FramePool + scored_df = framepool_caller(path) + + # save output + outpath = path.replace(".tsv",".framepool.tsv") + scored_df.to_csv(outpath, index=False, sep='\t') + print(f"Saved FramePool-annotated output to {outpath}.") + + else: + raise Exception("Input file must end with .tsv!") + +if __name__ == "__main__": + main() \ No newline at end of file diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..3f8ecf6 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,1123 @@ +[[package]] +name = "arrow" +version = "1.3.0" +description = "Better dates & times for Python" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +python-dateutil = ">=2.7.0" +types-python-dateutil = ">=2.8.10" + +[package.extras] +doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] +test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (>=3.0.0,<4.0.0)"] + +[[package]] +name = "attrs" +version = "23.1.0" +description = "Classes Without Boilerplate" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.extras] +cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] +dev = ["attrs[docs,tests]", "pre-commit"] +docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] +tests = ["attrs[tests-no-zope]", "zope-interface"] +tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] + +[[package]] +name = "binaryornot" +version = "0.4.4" +description = "Ultra-lightweight pure Python package to check if a file is binary or text." +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +chardet = ">=3.0.2" + +[[package]] +name = "certifi" +version = "2023.11.17" +description = "Python package for providing Mozilla's CA Bundle." +category = "main" +optional = false +python-versions = ">=3.6" + +[[package]] +name = "chardet" +version = "5.2.0" +description = "Universal encoding detector for Python 3" +category = "main" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "charset-normalizer" +version = "3.3.2" +description = "The Real First Universal Charset Detector. 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