From 237d25df53da73e7f3ef41717df141fb8945ba2e Mon Sep 17 00:00:00 2001 From: Josh Iszatt Date: Thu, 18 May 2023 10:00:24 +0000 Subject: [PATCH] ready for first container release --- README.md | 6 +- pip/LICENSE.md | 661 +++++++++++++++++++++ pip/Phanatic.egg-info/PKG-INFO | 18 + pip/Phanatic.egg-info/SOURCES.txt | 9 + pip/Phanatic.egg-info/dependency_links.txt | 1 + pip/Phanatic.egg-info/entry_points.txt | 2 + pip/Phanatic.egg-info/top_level.txt | 1 + pip/Phanatic/__init__.py | 0 pip/Phanatic/main.py | 108 ++++ pip/dist/Phanatic-2.2.0.tar.gz | Bin 0 -> 14614 bytes pip/setup.py | 30 + 11 files changed, 834 insertions(+), 2 deletions(-) create mode 100755 pip/LICENSE.md create mode 100644 pip/Phanatic.egg-info/PKG-INFO create mode 100644 pip/Phanatic.egg-info/SOURCES.txt create mode 100644 pip/Phanatic.egg-info/dependency_links.txt create mode 100644 pip/Phanatic.egg-info/entry_points.txt create mode 100644 pip/Phanatic.egg-info/top_level.txt create mode 100755 pip/Phanatic/__init__.py create mode 100755 pip/Phanatic/main.py create mode 100644 pip/dist/Phanatic-2.2.0.tar.gz create mode 100755 pip/setup.py diff --git a/README.md b/README.md index 4b2be88..523e5fd 100755 --- a/README.md +++ b/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 diff --git a/pip/LICENSE.md b/pip/LICENSE.md new file mode 100755 index 0000000..0ad25db --- /dev/null +++ b/pip/LICENSE.md @@ -0,0 +1,661 @@ + GNU AFFERO GENERAL PUBLIC LICENSE + Version 3, 19 November 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +. diff --git a/pip/Phanatic.egg-info/PKG-INFO b/pip/Phanatic.egg-info/PKG-INFO new file mode 100644 index 0000000..e07c521 --- /dev/null +++ b/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 diff --git a/pip/Phanatic.egg-info/SOURCES.txt b/pip/Phanatic.egg-info/SOURCES.txt new file mode 100644 index 0000000..f170603 --- /dev/null +++ b/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 \ No newline at end of file diff --git a/pip/Phanatic.egg-info/dependency_links.txt b/pip/Phanatic.egg-info/dependency_links.txt new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/pip/Phanatic.egg-info/dependency_links.txt @@ -0,0 +1 @@ + diff --git a/pip/Phanatic.egg-info/entry_points.txt b/pip/Phanatic.egg-info/entry_points.txt new file mode 100644 index 0000000..95c29b7 --- /dev/null +++ b/pip/Phanatic.egg-info/entry_points.txt @@ -0,0 +1,2 @@ +[console_scripts] +phanatic.py = Phanatic.main:main diff --git a/pip/Phanatic.egg-info/top_level.txt b/pip/Phanatic.egg-info/top_level.txt new file mode 100644 index 0000000..a2fb3e6 --- /dev/null +++ b/pip/Phanatic.egg-info/top_level.txt @@ -0,0 +1 @@ +Phanatic diff --git a/pip/Phanatic/__init__.py b/pip/Phanatic/__init__.py new file mode 100755 index 0000000..e69de29 diff --git a/pip/Phanatic/main.py b/pip/Phanatic/main.py new file mode 100755 index 0000000..1c58800 --- /dev/null +++ b/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 \ + $(docker run -d \ + -v {input_path}:/assemble/input \ + -v {output_path}:/assemble/output \ + {image} sleep 1d) bash") + else: + command = ["%s -v %s:/assemble/input -v %s:/assemble/output %s /assemble/bin/assemble.sh" % + (docker, input_path, output_path, image)] + result = subprocess.Popen(command, shell=True) + print(command) + + +if __name__ == "__main__": + exit(main()) \ No newline at end of file diff --git a/pip/dist/Phanatic-2.2.0.tar.gz b/pip/dist/Phanatic-2.2.0.tar.gz new file mode 100644 index 0000000000000000000000000000000000000000..d565f577d3733556ee4c14b388da6d4743ec39a8 GIT binary patch literal 14614 zcmV+xIqAk9iwFpd_GM%O|4?XQZeet3V=Xc+GA=MKbYXG;?S1=G8%MgRf9}7cOZRRW zs)RsbaN;bfC0LHN!N38WtZO$#jWjJZ>(PwPJiyx2{_ppD^o2eRyr6*c4Cxkk1}}*8RJ;cks;rH-6vW+wbo`(I1|ChEH8qQ32CG z`7%HIU+Gzu%*=8B=&NVX_71)}?DzH$zdk%TJW@|Kpa1Vam(wVVs${&g-`nr)?fzl( z|NQwO{@Z_kxEKEGXukjK*+Ku{`N4kw0OmNSrA3f1~pOgN-Q2wu1e7-+_t506N8eCoI?+53DtCKT*`Sv?N4K3)Q^y<%#rYMs< z(+6GM|5~5t_hvRSh2DqbS4yAe^F@)|O)I^1x=ml|SA{Y9I-gVzQDO9}yv|}k#ysol 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