ready for first container release

README.md

@@ -23,14 +23,16 @@ Iszatt J.(2023).Phanatic(v2.2.0)[Source code].Github:https://github.com/JoshuaIs
 ```
 
 ## Installation
+To run this pipeline you first need a working docker installation. 
+
 Install using pip
 ```sh
-
+pip install Phanatic==2.2.0
 ```
 
 Run the help command to see options 
 ```sh
-
+phanatic.py -h
 ```
 
 ## Output

pip/Phanatic.egg-info/PKG-INFO

@@ -0,0 +1,18 @@
+Metadata-Version: 2.1
+Name: Phanatic
+Version: 2.2.0
+Summary: Python package to run de novo bacteriophage assembly container.
+Home-page: https://github.com/JoshuaIszatt/Phanatic
+Author: Joshua Iszatt
+Author-email: joshiszatt@gmail.com
+License: AGPL-3.0
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: License :: OSI Approved :: GNU Affero General Public License v3
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Requires-Python: >=3.6
+License-File: LICENSE.md

pip/Phanatic.egg-info/SOURCES.txt

@@ -0,0 +1,9 @@
+LICENSE.md
+setup.py
+Phanatic/__init__.py
+Phanatic/main.py
+Phanatic.egg-info/PKG-INFO
+Phanatic.egg-info/SOURCES.txt
+Phanatic.egg-info/dependency_links.txt
+Phanatic.egg-info/entry_points.txt
+Phanatic.egg-info/top_level.txt

pip/Phanatic.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

pip/Phanatic.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+phanatic.py = Phanatic.main:main

pip/Phanatic.egg-info/top_level.txt

@@ -0,0 +1 @@
+Phanatic

pip/Phanatic/main.py

@@ -0,0 +1,108 @@
+def main():
+
+    import os
+    import sys
+    import subprocess
+    import argparse
+    import random
+    import pandas as pd
+
+    # Did you know prompts
+    prompts = [
+        "Phanatic currently only supports short, paired end, illumina reads (default 'PE_illumina_150').",
+        "I (J. Iszatt) made Phanatic to assemble S. aureus phage genomes as part of my PhD project.",
+        "This is a short read assembler primarily designed for bacteriophage",
+        "My favourite bacteriophage is a Silviavirus named Koomba-kaat_1",
+        "You can use your own config file to customise the assembly and functions"
+    ]
+    random_prompt = random.choice(prompts)
+
+    # Creating function to check directory path
+    def valid_dir(dir_path):
+        if not os.path.isdir(dir_path):
+            raise argparse.ArgumentTypeError(
+                f"{dir_path} is not a valid directory path")
+        if not os.access(dir_path, os.R_OK):
+            raise argparse.ArgumentTypeError(
+                f"{dir_path} is not a readable directory")
+        return dir_path
+
+    def valid_file(file_path):
+        if not os.path.isfile(file_path):
+            raise argparse.ArgumentTypeError(
+                f"{file_path} is not a valid file path")
+        if not os.access(file_path, os.R_OK):
+            raise argparse.ArgumentTypeError(
+                f"{file_path} is not a readable file")
+        return file_path
+
+    # Parsing arguments
+    image = 'iszatt/phanatic:2.2.0'
+    parser = argparse.ArgumentParser(description=f"Easy short read assembly. Joshua J Iszatt: https://github.com/JoshuaIszatt")
+
+    # Input/output options
+    parser.add_argument('-i', '--input', type=valid_dir, help='Input reads files')
+    parser.add_argument('-o', '--output', type=valid_dir, help='Direct output to this location')
+    parser.add_argument('-r', '--reads', type=str, choices=['PE_illumina_150'], default='PE_illumina_150', help='Pipeline options')
+    parser.add_argument('-c', '--config', type=valid_file, help='Use config file to customise assembly')
+    parser.add_argument('-v', '--version', action="store_true", help='Print the docker image version')
+    parser.add_argument('--show_console', action="store_true", help='Include this flag to write output to console')
+    parser.add_argument('--manual', action="store_true", help='Enter container interactively')
+    args = parser.parse_args()
+
+    # Printing version
+    if args.version:
+        print(image)
+        sys.exit(0)
+
+    # Obtaining absolute paths if entered correctly
+    if args.input and args.output:
+        input_path = os.path.abspath(args.input)
+        output_path = os.path.abspath(args.output)
+    elif args.input and not args.output:
+        sys.exit("No output directory specified\nRun --help to see options")
+    elif args.output and not args.input:
+        sys.exit("No input directory specified\nRun --help to see options")
+    else:
+        sys.exit("No input or output directories specified\nRun --help to see options")
+
+
+    # Printing command variables
+    print(
+        f"Program run: {image}",
+        f"Input path: {input_path}",
+        f"Output path: {output_path}",
+        f"Reads type: {args.reads}",
+        ">>>",
+        f"Did you know:",
+        f"{random_prompt}",
+        ">>>\n",
+        sep='\n'
+        )
+
+    # Copying config file to output dir
+    if args.config:
+        print(f"Using {args.config} file \n")
+        os.system(f"cp {args.config} {args.output}/config.ini")
+
+    if args.show_console:
+        docker = "docker run"
+    else:
+        docker = "docker run -d"
+
+    # Running docker
+    if args.manual: 
+        os.system(f"docker exec -it \
+            $(docker run -d \
+            -v {input_path}:/assemble/input \
+            -v {output_path}:/assemble/output \
+            {image} sleep 1d) bash")
+    else:
+        command = ["%s -v %s:/assemble/input -v %s:/assemble/output %s /assemble/bin/assemble.sh" %
+                (docker, input_path, output_path, image)]
+        result = subprocess.Popen(command, shell=True)
+        print(command)
+
+
+if __name__ == "__main__":
+    exit(main())

pip/setup.py

@@ -0,0 +1,30 @@
+from setuptools import find_packages, setup
+
+setup(
+    name="Phanatic",
+    version="2.2.0",
+    description="Python package to run de novo bacteriophage assembly container.",
+    url="https://github.com/JoshuaIszatt/Phanatic",
+    author="Joshua Iszatt",
+    author_email="joshiszatt@gmail.com",
+    license="AGPL-3.0",
+    classifiers=[
+        "Development Status :: 2 - Pre-Alpha",
+        "License :: OSI Approved :: GNU Affero General Public License v3",
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.6",
+        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+    ],
+    install_requires=[""],
+    python_requires=">=3.6",
+    packages=find_packages(),
+    data_files=[("", ["LICENSE.md"])],
+    entry_points={
+        'console_scripts': [
+            'phanatic.py = Phanatic.main:main',
+        ],
+    },
+)