Merge pull request #46 from AlexandrovLab/docker_cli

Add CLI and container updates

Dockerfile

@@ -0,0 +1,26 @@
+# Start with a base Ubuntu image and install Python
+FROM ubuntu:22.04
+
+# Avoid prompts from apt
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Install Python and other dependencies, and apply updates
+RUN apt-get update && apt-get upgrade -y && \
+    apt-get install -y python3-pip python3-dev && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+
+# Set the working directory in the container
+WORKDIR /usr/src/app
+
+# Install SigProfilerMatrixGenerator using pip
+RUN pip3 install SigProfilerPlotting==1.3.21
+
+# Create a non-root user named 'spm_user'
+RUN useradd -m -s /bin/bash spm_user
+
+# Change the ownership of the /usr/src/app directory and its contents to the new non-root user
+RUN chown -R spm_user:spm_user /usr/src/app
+
+# Switch to the non-root user for subsequent commands and when running the container
+USER spm_user

MANIFEST.in

@@ -1,3 +1,4 @@
 include sigProfilerPlotting/fonts/*
 include sigProfilerPlotting/reference_formats/*
+include sigProfilerPlotting/controllers/*
 include tests/*

README.md

@@ -26,17 +26,23 @@ This section will guide you through the minimum steps required to plot mutationa
                           pip install SigProfilerPlotting
 ```
 
-2. From within a python session, you can now plot your mutational matrices as follows:
+2. Plot mutational matrices from a Python session or using the Command Line Interface (CLI) as follows:
+
+Using the Python session, the command is as follows:
  ```python
 $ python3
 >> import sigProfilerPlotting as sigPlt
 >> sigPlt.plotSBS(matrix_path, output_path, project, plot_type, percentage=False)
  ```
- The available functions are listed below and the layout of the required parameters are as follows:
 
-      sigPlt.plotSBS(matrix_path, output_path, project, plot_type)
+The required parameters are:
+
+    sigPlt.plotSBS(matrix_path, output_path, project, plot_type)
 
-where matrix_path, output_path, project, and plot_type must be strings (surrounded by quotation marks, ex: "/Users/ebergstr/Desktop/test_sample").   
+Using the CLI, the command is as follows:
+```bash
+SigProfilerPlotting plotSBS <matrix_path> <output_path> <project> <plot_type>
+```
 
  3. The final plots are saved into the user-provided output folder.
 

setup.py

@@ -14,7 +14,7 @@ def readme():
         return f.read()
 
 
-VERSION = "1.3.20"
+VERSION = "1.3.21"
 
 
 def write_version_py(filename="sigProfilerPlotting/version.py"):
@@ -23,7 +23,7 @@ def write_version_py(filename="sigProfilerPlotting/version.py"):
 # THIS FILE IS GENERATED FROM SIGPROFILERPLOTTING SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
-update = 'Upgrade v1.3.20: Add np.ndarray to process_input'
+update = 'Upgrade v1.3.21: Add CLI and container updates'
     
     """
     fh = open(filename, "w")
@@ -56,6 +56,7 @@ def write_version_py(filename="sigProfilerPlotting/version.py"):
         "sigProfilerPlotting",
         "sigProfilerPlotting.reference_formats",
         "sigProfilerPlotting.fonts",
+        "sigProfilerPlotting.controllers",
     ],
     install_requires=[
         "matplotlib>=3.4.3",
@@ -70,6 +71,11 @@ def write_version_py(filename="sigProfilerPlotting/version.py"):
             "numpy>=1.21.2",
         ],
     },
+    entry_points={
+        "console_scripts": [
+            "SigProfilerPlotting=sigProfilerPlotting.sigProfilerPlotting_CLI:main_function",
+        ],
+    },
     package_data={"": ["fonts/*.ttf"]},
     include_package_data=True,
     zip_safe=False,

sigProfilerPlotting/controllers/__init__.py

@@ -0,0 +1 @@
+import sigProfilerPlotting

sigProfilerPlotting/controllers/cli_controller.py

@@ -0,0 +1,231 @@
+import argparse
+from typing import List
+import sigProfilerPlotting as sigPlt
+
+
+# Common parser setup for shared arguments
+def common_plotting_arguments(parser):
+    parser.add_argument("matrix_path", help="The path to the input matrix file.")
+    parser.add_argument(
+        "output_path", help="The directory where the plots will be saved."
+    )
+    parser.add_argument("project", help="The name of the project.")
+    parser.add_argument("plot_type", help="The type of plot to generate.")
+    parser.add_argument(
+        "--percentage", action="store_true", help="Display percentages in the plot."
+    )
+    parser.add_argument(
+        "--custom_text_upper", help="Custom text to display at the top of the plot."
+    )
+    parser.add_argument(
+        "--custom_text_middle", help="Custom text to display in the middle of the plot."
+    )
+    parser.add_argument(
+        "--custom_text_bottom", help="Custom text to display at the bottom of the plot."
+    )
+    parser.add_argument(
+        "--savefig_format",
+        default="pdf",
+        choices=["pdf", "png", "pil_image"],
+        help="The file format for saving the plot.",
+    )
+    parser.add_argument("--volume", help="Specify a volume for Docker container usage.")
+    parser.add_argument(
+        "--dpi",
+        type=int,
+        default=100,
+        help="The resolution of the plot in dots per inch.",
+    )
+
+
+def parse_arguments_sbs(args: List[str]) -> argparse.Namespace:
+    parser = argparse.ArgumentParser(
+        prog="SigProfilerPlotting plotDBS", description="Generate DBS plots."
+    )
+    common_plotting_arguments(parser)
+    return parser.parse_args(args)
+
+
+def parse_arguments_id(args: List[str]) -> argparse.Namespace:
+    parser = argparse.ArgumentParser(
+        prog="SigProfilerPlotting plotID", description="Generate ID plots."
+    )
+    common_plotting_arguments(parser)
+    return parser.parse_args(args)
+
+
+def parse_arguments_dbs(args: List[str]) -> argparse.Namespace:
+    parser = argparse.ArgumentParser(
+        prog="SigProfilerPlotting plotDBS", description="Generate DBS plots."
+    )
+    common_plotting_arguments(parser)
+    return parser.parse_args(args)
+
+
+def parse_arguments_sv(args: List[str]) -> argparse.Namespace:
+    parser = argparse.ArgumentParser(
+        prog="SigProfilerPlotting plotSV", description="Generate SV plots."
+    )
+    parser.add_argument("matrix_path", help="The path to the input matrix file.")
+    parser.add_argument(
+        "output_path", help="The directory where the plots will be saved."
+    )
+    parser.add_argument("project", help="The name of the project.")
+    parser.add_argument(
+        "--percentage", action="store_true", help="Display percentages in the plot."
+    )
+    parser.add_argument(
+        "--aggregate", action="store_true", help="Aggregate all samples."
+    )
+    parser.add_argument(
+        "--savefig_format",
+        default="pdf",
+        choices=["pdf", "png", "pil_image"],
+        help="The file format for saving the plot.",
+    )
+    parser.add_argument(
+        "--dpi",
+        type=int,
+        default=100,
+        help="The resolution of the plot in dots per inch.",
+    )
+    return parser.parse_args(args)
+
+
+def parse_arguments_cnv(args: List[str]) -> argparse.Namespace:
+    parser = argparse.ArgumentParser(
+        prog="SigProfilerPlotting plotCNV", description="Generate CNV plots."
+    )
+    parser.add_argument("matrix_path", help="The path to the input matrix file.")
+    parser.add_argument(
+        "output_path", help="The directory where the plots will be saved."
+    )
+    parser.add_argument("project", help="The name of the project.")
+    parser.add_argument(
+        "--percentage", action="store_true", help="Display percentages in the plot."
+    )
+    parser.add_argument(
+        "--aggregate", action="store_true", help="Aggregate data for the plot."
+    )
+    parser.add_argument(
+        "--read_from_file",
+        action="store_true",
+        default=True,
+        help="Read data from a file for the plot.",
+    )
+    parser.add_argument(
+        "--savefig_format",
+        default="pdf",
+        choices=["pdf", "png", "pil_image"],
+        help="The file format for saving the plot.",
+    )
+    parser.add_argument(
+        "--dpi",
+        type=int,
+        default=100,
+        help="The resolution of the plot in dots per inch.",
+    )
+    return parser.parse_args(args)
+
+
+def dispatch_plot_sbs(parsed_args: argparse.Namespace) -> None:
+    sigPlt.plotSBS(
+        matrix_path=parsed_args.matrix_path,
+        output_path=parsed_args.output_path,
+        project=parsed_args.project,
+        plot_type=parsed_args.plot_type,
+        percentage=parsed_args.percentage,
+        custom_text_upper=parsed_args.custom_text_upper,
+        custom_text_middle=parsed_args.custom_text_middle,
+        custom_text_bottom=parsed_args.custom_text_bottom,
+        savefig_format=parsed_args.savefig_format,
+        volume=parsed_args.volume,
+        dpi=parsed_args.dpi,
+    )
+
+
+def dispatch_plot_id(parsed_args: argparse.Namespace) -> None:
+    sigPlt.plotID(
+        matrix_path=parsed_args.matrix_path,
+        output_path=parsed_args.output_path,
+        project=parsed_args.project,
+        plot_type=parsed_args.plot_type,
+        percentage=parsed_args.percentage,
+        custom_text_upper=parsed_args.custom_text_upper,
+        custom_text_middle=parsed_args.custom_text_middle,
+        custom_text_bottom=parsed_args.custom_text_bottom,
+        savefig_format=parsed_args.savefig_format,
+        volume=parsed_args.volume,
+        dpi=parsed_args.dpi,
+    )
+
+
+def dispatch_plot_dbs(parsed_args: argparse.Namespace) -> None:
+    sigPlt.plotDBS(
+        matrix_path=parsed_args.matrix_path,
+        output_path=parsed_args.output_path,
+        project=parsed_args.project,
+        plot_type=parsed_args.plot_type,
+        percentage=parsed_args.percentage,
+        custom_text_upper=parsed_args.custom_text_upper,
+        custom_text_middle=parsed_args.custom_text_middle,
+        custom_text_bottom=parsed_args.custom_text_bottom,
+        savefig_format=parsed_args.savefig_format,
+        volume=parsed_args.volume,
+        dpi=parsed_args.dpi,
+    )
+
+
+def dispatch_plot_sv(parsed_args: argparse.Namespace) -> None:
+    sigPlt.plotSV(
+        matrix_path=parsed_args.matrix_path,
+        output_path=parsed_args.output_path,
+        project=parsed_args.project,
+        percentage=parsed_args.percentage,
+        aggregate=parsed_args.aggregate,
+        savefig_format=parsed_args.savefig_format,
+        dpi=parsed_args.dpi,
+    )
+
+
+def dispatch_plot_cnv(parsed_args: argparse.Namespace) -> None:
+    sigPlt.plotCNV(
+        matrix_path=parsed_args.matrix_path,
+        output_path=parsed_args.output_path,
+        project=parsed_args.project,
+        percentage=parsed_args.percentage,
+        aggregate=parsed_args.aggregate,
+        read_from_file=parsed_args.read_from_file,
+        savefig_format=parsed_args.savefig_format,
+        dpi=parsed_args.dpi,
+    )
+
+
+class CliController:
+    def dispatch(self, user_args: List[str]):
+        if "plotSBS" in user_args:
+            parsed_args = parse_arguments_sbs(user_args[1:])
+            dispatch_plot_sbs(parsed_args)
+        elif "plotID" in user_args:
+            parsed_args = parse_arguments_id(user_args[1:])
+            dispatch_plot_id(parsed_args)
+        elif "plotDBS" in user_args:
+            parsed_args = parse_arguments_dbs(user_args[1:])
+            dispatch_plot_dbs(parsed_args)
+        elif "plotSV" in user_args:
+            parsed_args = parse_arguments_sv(user_args[1:])
+            dispatch_plot_sv(parsed_args)
+        elif "plotCNV" in user_args:
+            parsed_args = parse_arguments_cnv(user_args[1:])
+            dispatch_plot_cnv(parsed_args)
+        else:
+            print(
+                "Unknown command. Available commands: plotSBS, plotID, plotDBS, plotSV, plotCNV."
+            )
+
+
+if __name__ == "__main__":
+    import sys
+
+    controller = CliController()
+    controller.dispatch(sys.argv)

sigProfilerPlotting/sigProfilerPlotting_CLI.py

@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+
+import sys
+from sigProfilerPlotting import sigProfilerPlotting
+from sigProfilerPlotting.controllers import cli_controller
+
+
+def main_function():
+    commands = {
+        "plotSBS": "Plot Single Base Substitutions.",
+        "plotID": "Plot Small Insertions and Deletions.",
+        "plotDBS": "Plot Doublet Base Substitutions.",
+        "plotSV": "Plot Structural Variations.",
+        "plotCNV": "Plot Copy Number Variations.",
+    }
+
+    if len(sys.argv) < 2 or sys.argv[1] not in commands.keys():
+        print_usage(commands)
+        sys.exit(1)
+
+    command = sys.argv[1]
+    args = sys.argv[1:]
+
+    controller = cli_controller.CliController()
+    valid_commands = {"plotSBS", "plotID", "plotDBS", "plotSV", "plotCNV"}
+
+    if command in valid_commands:
+        controller.dispatch(args)
+    else:
+        print_usage(commands)
+        sys.exit(1)
+
+
+def print_usage(commands):
+    """Prints the usage message."""
+    print("Usage: SigProfilerPlotting <command> [<args>]\n")
+    print("Commands:")
+    for cmd, desc in commands.items():
+        print(f"  {cmd}: {desc}")
+    print(
+        "\nUse 'SigProfilerPlotting <command> --help' for more information on a specific command."
+    )
+
+
+if __name__ == "__main__":
+    main_function()