MitoBee 1.0.post0__tar.gz

mitobee-1.0.post0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Bhavya Papudeshi
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

mitobee-1.0.post0/MitoBee.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: MitoBee
+Version: 1.0.post0
+Summary: Build mitogenomes from WGS metagenomes
+Author-email: Bhavya Papudeshi <bnalaga1@unil.ch>
+License: MIT
+Classifier: Environment :: Console
+Classifier: Environment :: MacOS X
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: snaketool-utils>=0.0.5
+Requires-Dist: snakemake>=8.28.0
+Requires-Dist: snakemake-executor-plugin-slurm
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: Click>=8.1.3
+Requires-Dist: metasnek>=0.0.8
+Requires-Dist: attrmap>=0.0.7
+Requires-Dist: biopython>=1.8.1
+Requires-Dist: pandas
+Requires-Dist: matplotlib
+Requires-Dist: snakemake-executor-plugin-slurm>=0.5.1
+Dynamic: license-file
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+[![](https://img.shields.io/static/v1?label=CLI&message=Snaketool&color=blueviolet)](https://github.com/beardymcjohnface/Snaketool)
+![GitHub last commit (branch)](https://img.shields.io/github/last-commit/npbhavya/MitoBee?branch=main)
+
+<img src="test-files/mitobeelogo.png" width="200" alt="MitoBee logo">
+
+# MitoBee
+
+## Snakemake workflow to get mitogenomes from metagenomic data
+Still under development! Stable release out as a version, but only if there is a closely related mitogenome available.
+
+Documentation: [Wiki](https://github.com/npbhavya/Mitobee/wiki/Home)
+
+### Install 
+
+**Source install**
+Run the below commands:
+
+    git clone https://github.com/npbhavya/MitoBee.git
+    cd MitBee
+    mamba create -y -n mitobee python=3.13
+    conda activate mitobee
+    pip install -e . 
+
+**Once I have a stable version release, I will upload them to conda and pip as well**
+
+### Running the code
+Note: This code works only on paired end metagenomes for now. 
+
+This workflow is made modular; 
+
+1. `mitobee run` 
+If there is a representative closely related genome mitogenome, provide that as the host seq and get started
+
+```
+    #Running mitobee with test files available in the repo
+    mitobee run --input test-files/metagenomes --extn fastq.gz \
+         --pattern_r1 _R1 --pattern_r2 _R2 \
+         --host_seq test-files/am-dh4.fasta \
+         --output output
+```
+
+2. `mitobee tree`
+Once the mitochondrial genomes are built from each metagenome sample, run this module to build a tree with these mitogenomes and other references
+
+```
+    #After the mitogenomes are made from the mitobee run results. Add other references to build a tree
+    #Once again example with test files
+    mitobee tree --input test-files/mitogenomes --extn fasta --output output -k all
+
+```
+
+3.  `mitobee search`
+If there is a no closely related mitogenome available, then this step can be run first to search against a set of mitogenomes or mito genes 
+This module will provide an overview of which reference to use
+
+```
+    #If a closely related mitochondrial genome is not available, but a gene is, like cox  or rRNA genes
+    #Download the reference genes you would like to use of the closely related genomes
+
+    #to search against mitogenomes refernece set
+    mitobee search --input test-files/mitogenomes --extn fastq.gz \
+        --pattern_r1 _R1 --pattern_r2 _R2 \
+        --ref_seq  test-files/ref-set-genome --output output \
+        -k all --mode mitogenome
+
+    #to search against mitogenomes refernece gene set 
+    mitobee search --input test-files/mitogenomes --extn fastq.gz \
+        --pattern_r1 _R1 --pattern_r2 _R2 \
+        --ref_seq  test-files/ref-set-genes --output output \
+        -k all --mode genes 
+
+```
+
+### Input files
+Input files:
+- Input directory with metagenomes
+- Reference directory
+  - If running `run`  or `tree` module, provide a **(one)** reference genome. 
+  - If running `gene` module, provide a reference gene set
+
+### Output files
+Output files: Provide the output folder, contains subdirectories
+- PROCESSING: Folder containing intermediate files
+- REPORTS: Final results including the mitogenome fasta files from (hopefully) each metagenome sample \
+      Also inlcudes the QC reports, to include stats on how many reads were processed, and not

mitobee-1.0.post0/MitoBee.egg-info/SOURCES.txt

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+LICENSE
+README.md
+pyproject.toml
+MitoBee.egg-info/PKG-INFO
+MitoBee.egg-info/SOURCES.txt
+MitoBee.egg-info/dependency_links.txt
+MitoBee.egg-info/entry_points.txt
+MitoBee.egg-info/requires.txt
+MitoBee.egg-info/top_level.txt
+mitobee/__init__.py
+mitobee/__main__.py
+mitobee/_version.py

mitobee-1.0.post0/MitoBee.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

mitobee-1.0.post0/MitoBee.egg-info/entry_points.txt

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+[console_scripts]
+mitobee = mitobee.__main__:main

mitobee-1.0.post0/MitoBee.egg-info/requires.txt

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+snaketool-utils>=0.0.5
+snakemake>=8.28.0
+snakemake-executor-plugin-slurm
+pyyaml>=6.0
+Click>=8.1.3
+metasnek>=0.0.8
+attrmap>=0.0.7
+biopython>=1.8.1
+pandas
+matplotlib
+snakemake-executor-plugin-slurm>=0.5.1

mitobee-1.0.post0/MitoBee.egg-info/top_level.txt

@@ -0,0 +1 @@
+mitobee

mitobee-1.0.post0/PKG-INFO

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+Metadata-Version: 2.4
+Name: MitoBee
+Version: 1.0.post0
+Summary: Build mitogenomes from WGS metagenomes
+Author-email: Bhavya Papudeshi <bnalaga1@unil.ch>
+License: MIT
+Classifier: Environment :: Console
+Classifier: Environment :: MacOS X
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: snaketool-utils>=0.0.5
+Requires-Dist: snakemake>=8.28.0
+Requires-Dist: snakemake-executor-plugin-slurm
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: Click>=8.1.3
+Requires-Dist: metasnek>=0.0.8
+Requires-Dist: attrmap>=0.0.7
+Requires-Dist: biopython>=1.8.1
+Requires-Dist: pandas
+Requires-Dist: matplotlib
+Requires-Dist: snakemake-executor-plugin-slurm>=0.5.1
+Dynamic: license-file
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+[![](https://img.shields.io/static/v1?label=CLI&message=Snaketool&color=blueviolet)](https://github.com/beardymcjohnface/Snaketool)
+![GitHub last commit (branch)](https://img.shields.io/github/last-commit/npbhavya/MitoBee?branch=main)
+
+<img src="test-files/mitobeelogo.png" width="200" alt="MitoBee logo">
+
+# MitoBee
+
+## Snakemake workflow to get mitogenomes from metagenomic data
+Still under development! Stable release out as a version, but only if there is a closely related mitogenome available.
+
+Documentation: [Wiki](https://github.com/npbhavya/Mitobee/wiki/Home)
+
+### Install 
+
+**Source install**
+Run the below commands:
+
+    git clone https://github.com/npbhavya/MitoBee.git
+    cd MitBee
+    mamba create -y -n mitobee python=3.13
+    conda activate mitobee
+    pip install -e . 
+
+**Once I have a stable version release, I will upload them to conda and pip as well**
+
+### Running the code
+Note: This code works only on paired end metagenomes for now. 
+
+This workflow is made modular; 
+
+1. `mitobee run` 
+If there is a representative closely related genome mitogenome, provide that as the host seq and get started
+
+```
+    #Running mitobee with test files available in the repo
+    mitobee run --input test-files/metagenomes --extn fastq.gz \
+         --pattern_r1 _R1 --pattern_r2 _R2 \
+         --host_seq test-files/am-dh4.fasta \
+         --output output
+```
+
+2. `mitobee tree`
+Once the mitochondrial genomes are built from each metagenome sample, run this module to build a tree with these mitogenomes and other references
+
+```
+    #After the mitogenomes are made from the mitobee run results. Add other references to build a tree
+    #Once again example with test files
+    mitobee tree --input test-files/mitogenomes --extn fasta --output output -k all
+
+```
+
+3.  `mitobee search`
+If there is a no closely related mitogenome available, then this step can be run first to search against a set of mitogenomes or mito genes 
+This module will provide an overview of which reference to use
+
+```
+    #If a closely related mitochondrial genome is not available, but a gene is, like cox  or rRNA genes
+    #Download the reference genes you would like to use of the closely related genomes
+
+    #to search against mitogenomes refernece set
+    mitobee search --input test-files/mitogenomes --extn fastq.gz \
+        --pattern_r1 _R1 --pattern_r2 _R2 \
+        --ref_seq  test-files/ref-set-genome --output output \
+        -k all --mode mitogenome
+
+    #to search against mitogenomes refernece gene set 
+    mitobee search --input test-files/mitogenomes --extn fastq.gz \
+        --pattern_r1 _R1 --pattern_r2 _R2 \
+        --ref_seq  test-files/ref-set-genes --output output \
+        -k all --mode genes 
+
+```
+
+### Input files
+Input files:
+- Input directory with metagenomes
+- Reference directory
+  - If running `run`  or `tree` module, provide a **(one)** reference genome. 
+  - If running `gene` module, provide a reference gene set
+
+### Output files
+Output files: Provide the output folder, contains subdirectories
+- PROCESSING: Folder containing intermediate files
+- REPORTS: Final results including the mitogenome fasta files from (hopefully) each metagenome sample \
+      Also inlcudes the QC reports, to include stats on how many reads were processed, and not

mitobee-1.0.post0/README.md

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+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+[![](https://img.shields.io/static/v1?label=CLI&message=Snaketool&color=blueviolet)](https://github.com/beardymcjohnface/Snaketool)
+![GitHub last commit (branch)](https://img.shields.io/github/last-commit/npbhavya/MitoBee?branch=main)
+
+<img src="test-files/mitobeelogo.png" width="200" alt="MitoBee logo">
+
+# MitoBee
+
+## Snakemake workflow to get mitogenomes from metagenomic data
+Still under development! Stable release out as a version, but only if there is a closely related mitogenome available.
+
+Documentation: [Wiki](https://github.com/npbhavya/Mitobee/wiki/Home)
+
+### Install 
+
+**Source install**
+Run the below commands:
+
+    git clone https://github.com/npbhavya/MitoBee.git
+    cd MitBee
+    mamba create -y -n mitobee python=3.13
+    conda activate mitobee
+    pip install -e . 
+
+**Once I have a stable version release, I will upload them to conda and pip as well**
+
+### Running the code
+Note: This code works only on paired end metagenomes for now. 
+
+This workflow is made modular; 
+
+1. `mitobee run` 
+If there is a representative closely related genome mitogenome, provide that as the host seq and get started
+
+```
+    #Running mitobee with test files available in the repo
+    mitobee run --input test-files/metagenomes --extn fastq.gz \
+         --pattern_r1 _R1 --pattern_r2 _R2 \
+         --host_seq test-files/am-dh4.fasta \
+         --output output
+```
+
+2. `mitobee tree`
+Once the mitochondrial genomes are built from each metagenome sample, run this module to build a tree with these mitogenomes and other references
+
+```
+    #After the mitogenomes are made from the mitobee run results. Add other references to build a tree
+    #Once again example with test files
+    mitobee tree --input test-files/mitogenomes --extn fasta --output output -k all
+
+```
+
+3.  `mitobee search`
+If there is a no closely related mitogenome available, then this step can be run first to search against a set of mitogenomes or mito genes 
+This module will provide an overview of which reference to use
+
+```
+    #If a closely related mitochondrial genome is not available, but a gene is, like cox  or rRNA genes
+    #Download the reference genes you would like to use of the closely related genomes
+
+    #to search against mitogenomes refernece set
+    mitobee search --input test-files/mitogenomes --extn fastq.gz \
+        --pattern_r1 _R1 --pattern_r2 _R2 \
+        --ref_seq  test-files/ref-set-genome --output output \
+        -k all --mode mitogenome
+
+    #to search against mitogenomes refernece gene set 
+    mitobee search --input test-files/mitogenomes --extn fastq.gz \
+        --pattern_r1 _R1 --pattern_r2 _R2 \
+        --ref_seq  test-files/ref-set-genes --output output \
+        -k all --mode genes 
+
+```
+
+### Input files
+Input files:
+- Input directory with metagenomes
+- Reference directory
+  - If running `run`  or `tree` module, provide a **(one)** reference genome. 
+  - If running `gene` module, provide a reference gene set
+
+### Output files
+Output files: Provide the output folder, contains subdirectories
+- PROCESSING: Folder containing intermediate files
+- REPORTS: Final results including the mitogenome fasta files from (hopefully) each metagenome sample \
+      Also inlcudes the QC reports, to include stats on how many reads were processed, and not

mitobee-1.0.post0/mitobee/__main__.py

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+"""
+Entrypoint for this workflow
+
+Check out the wiki for a detailed look at customising this file:
+https://github.com/beardymcjohnface/Snaketool/wiki/Customising-your-Snaketool
+"""
+
+import os
+import click
+from shutil import copyfile
+from snaketool_utils.cli_utils import OrderedCommands, run_snakemake, copy_config, echo_click
+
+"""Get the filepath to a Snaketool system file (relative to __main__.py)"""
+PACKAGE_DIR = os.path.dirname(os.path.realpath(__file__))
+PROJECT_ROOT = os.path.dirname(PACKAGE_DIR)  # one level up
+
+def snake_base(rel_path):
+    """Get the filepath to a project file relative to the repo root."""
+    return os.path.join(PROJECT_ROOT, rel_path)
+
+def get_version():
+    try:
+        from mitobee._version import version
+    except Exception:
+        version = "0.1.0"
+    return version
+
+
+def print_citation():
+    with open(snake_base("../MitoBee.CITATION"), "r") as f:
+        for line in f:
+            echo_click(line)
+
+
+def default_to_output(ctx, param, value):
+    """Callback for click options; places value in output directory unless specified"""
+    if param.default == value:
+        return os.path.join(ctx.params["output"], value)
+    return value
+
+# This is to ensure that the output directory gets generated if it hasnt already been generated
+def ensure_directory_exists(directory):
+    if not os.path.exists(directory):
+        os.makedirs(directory)
+
+def common_options(func):
+    """Common command line args
+    Define common command line args here, and include them with the @common_options decorator below.
+    """
+    options = [
+        click.option('--input', '_input', help='Directory of reads', type=click.Path(), required=False, default='testReads/paired', show_default=True),
+        click.option('--extn', 'extn',  help='Reads extension; fastq, fq, fastq.gz', type=click.Path(), required=False, default='fastq', show_default=True),
+        click.option('--pattern_r1', 'r1', help='Pattern to identify R1 reads (for paired-end data)', default='_R1', show_default=True),
+        click.option('--pattern_r2', 'r2', help='Pattern to identify R2 reads (for paired-end data)', default='_R2', show_default=True),
+        click.option('--host_seq', 'host_seq', help='Path to host genome index for host read removal', type=click.Path(), show_default=True),
+        click.option('--mode', type=click.Choice(['mitogenome', 'gene'], case_sensitive=False), help='Reference search mode either gene or mitochondrial genome', required=False),
+        click.option('--ref_set', 'refdb', help='Path to reference database of mitochondrial genomes or mitochondrial genes', type=click.Path(), required=False, show_default=True),
+        click.option('--output', 'output', help='Output directory', type=click.Path(),
+                     default='output', show_default=True),
+        click.option("--configfile", default="config.yaml", show_default=False, callback=default_to_output,
+                     help="Custom config file [default: config.yaml]"),
+        click.option('--threads', help='Number of threads to use', default=1, show_default=True),
+        click.option('--profile', help='Snakemake profile', default=None, show_default=False),
+        click.option('--db_dir', 'db_dir', help='Custom database directory', type=click.Path(), required=False),
+        click.option('--temp-dir', help='Temp directory', required=False),
+        click.option('--snake-default', multiple=True,
+                     default=['--rerun-incomplete', '--printshellcmds', '--nolock', '--show-failed-logs'],
+                     help="Customise Snakemake runtime args", show_default=True),
+        click.option("--log", default="mitobee.log", callback=default_to_output, hidden=True,),
+        click.option('--use-conda', default=True, help='Use conda for Snakemake rules',
+                     show_default=True),
+        click.option('--conda-frontend', default='mamba', help='Use mamba for Snakemake rules',
+                     show_default=True),
+        click.option('--conda-prefix', default=snake_base(os.path.join('workflow', 'conda')),
+                     help='Custom conda env directory', type=click.Path(), show_default=True),
+        click.option("--system-config", default=snake_base(os.path.join("..","config", "config.yaml")),hidden=True,),
+        click.argument("snake_args", nargs=-1),
+    ]
+    for option in reversed(options):
+        func = option(func)
+    return func
+
+
+@click.group(cls=OrderedCommands, context_settings=dict(help_option_names=["-h", "--help"]))
+@click.version_option(get_version(), "-v", "--version", is_flag=True)
+def cli():
+    """ Extract and assemble host mitochondrial genomes from metagenomic sequencing data.
+    \b
+    For more options, run:
+    mitobee --help"""
+    pass
+
+
+help_msg_run = """
+\b
+RUN EXAMPLES 
+mitobee run --input <input directory with metagenome reads> --pattern_r1 R1 --patern_r2 R2 --extn fq --host_seq <path to host mitochondrial genome> --sequencing paired --output <output directory> -k
+"""
+@click.command(epilog=help_msg_run, 
+    context_settings=dict(help_option_names=["-h", "--help"], ignore_unknown_options=True)
+    )
+
+@common_options
+def run(_input, extn, r1, r2, host_seq, output, temp_dir, configfile, conda_frontend, **kwargs):
+    """Run mitobee workflow"""
+    copy_config(configfile, system_config=snake_base(os.path.join('config', 'config.yaml')))
+
+    if not host_seq:
+        raise click.UsageError("Option --host_seq is required for 'mitobee run'.")
+    
+    merge_config = {
+        "args": {
+            "input": _input, 
+            "output": output, 
+            "extn": extn,
+            "pattern_r1": r1,
+            "pattern_r2": r2,
+            "host_seq": host_seq,
+            "configfile": configfile,
+            "temp_dir": temp_dir,
+        }
+    }
+
+    snake_default = list(kwargs.get('snake_default', []))
+    if conda_frontend and not any('--conda-frontend' in str(arg) for arg in snake_default):
+        snake_default.extend(['--conda-frontend', conda_frontend])
+    kwargs['snake_default'] = tuple(snake_default)
+
+    # run!
+    run_snakemake(
+        snakefile_path=snake_base(os.path.join('workflow', 'Snakefile')),
+        configfile=configfile,
+        merge_config=merge_config,
+        **kwargs
+    )
+
+help_msg_run = """
+\b
+TREE EXAMPLES 
+mitobee tree --input output/REPORTS/mitogenome --extn fasta --host_seq test-files/am-dh4.fasta --output output -k
+"""
+@click.command(epilog=help_msg_run, 
+    context_settings=dict(help_option_names=["-h", "--help"], ignore_unknown_options=True)
+    )
+
+@common_options
+def tree(_input, extn, output, temp_dir, configfile, conda_frontend, **kwargs):
+    """Run mitobee workflow"""
+    copy_config(configfile, system_config=snake_base(os.path.join('config', 'config.yaml')))
+
+    merge_config = {
+        "args": {
+            "input": _input, 
+            "output": output, 
+            "extn": extn,
+            "configfile": configfile,
+            "temp_dir": temp_dir,
+        }
+    }
+
+    snake_default = list(kwargs.get('snake_default', []))
+    if conda_frontend and not any('--conda-frontend' in str(arg) for arg in snake_default):
+        snake_default.extend(['--conda-frontend', conda_frontend])
+    kwargs['snake_default'] = tuple(snake_default)
+
+    # run!
+    run_snakemake(
+        snakefile_path=snake_base(os.path.join('workflow', 'TreeBuild.Snakefile')),
+        configfile=configfile,
+        merge_config=merge_config,
+        targets=["all"], 
+        **kwargs
+    )
+
+help_msg_run = """
+\b
+SEARCH EXAMPLES 
+mitobee search --input <input directory with metagenome reads> --extn fastq.gz --pattern_r1 R1 --patern_r2 R2 --ref_set test-files/ref-db --output output -k
+"""
+@click.command(epilog=help_msg_run, 
+    context_settings=dict(help_option_names=["-h", "--help"], ignore_unknown_options=True)
+    )
+
+@common_options
+def search(_input, extn, r1, r2, refdb, mode, output, temp_dir, configfile, conda_frontend, **kwargs):
+    """Run mitobee workflow"""
+    copy_config(configfile, system_config=snake_base(os.path.join('config', 'config.yaml')))
+    
+    merge_config = {
+        "args": {
+            "input": _input, 
+            "output": output, 
+            "extn": extn,
+            "pattern_r1": r1,
+            "pattern_r2": r2,
+            "ref_set": refdb,
+            "configfile": configfile,
+            "temp_dir": temp_dir,
+            "mode": mode,
+        }
+    }
+
+    snake_default = list(kwargs.get('snake_default', []))
+    if conda_frontend and not any('--conda-frontend' in str(arg) for arg in snake_default):
+        snake_default.extend(['--conda-frontend', conda_frontend])
+    kwargs['snake_default'] = tuple(snake_default)
+
+    # run!
+    run_snakemake(
+        snakefile_path=snake_base(os.path.join('workflow', 'Search.Snakefile')),
+        configfile=configfile,
+        merge_config=merge_config,
+        targets=["all"], 
+        **kwargs
+    )
+
+@click.command()
+@click.option('--configfile', default='config.yaml', help='Copy template config to file', show_default=True)
+def config(configfile, **kwargs):
+    """Copy the system default config file"""
+    copy_config(configfile, system_config=snake_base(os.path.join('config', 'config.yaml')))
+
+
+@click.command()
+def citation(**kwargs):
+    """Print the citation(s) for this tool"""
+    print_citation()
+
+
+cli.add_command(run)
+cli.add_command(tree)
+cli.add_command(search)
+cli.add_command(config)
+cli.add_command(citation)
+
+def main():
+    cli()
+
+if __name__ == '__main__':
+    main()

mitobee-1.0.post0/mitobee/_version.py

@@ -0,0 +1,34 @@
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '1.0.post0'
+__version_tuple__ = version_tuple = (1, 0, 'post0')
+
+__commit_id__ = commit_id = 'g7609bb359'

mitobee-1.0.post0/pyproject.toml

@@ -0,0 +1,53 @@
+[build-system]
+requires = ["setuptools>=69", "setuptools_scm", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "MitoBee"
+dynamic = ["version"]
+description = "Build mitogenomes from WGS metagenomes"
+readme = { file = "README.md", content-type = "text/markdown" }
+authors = [
+    { name = "Bhavya Papudeshi", email = "bnalaga1@unil.ch" }
+]
+
+license = { text = "MIT" }
+classifiers = [
+    "Environment :: Console",
+    "Environment :: MacOS X",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Natural Language :: English",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Bio-Informatics"
+]
+requires-python = ">=3.9"
+dependencies = [
+    "snaketool-utils>=0.0.5",
+    "snakemake>=8.28.0",
+    "snakemake-executor-plugin-slurm",
+    "pyyaml>=6.0",
+    "Click>=8.1.3",
+    "metasnek>=0.0.8",
+    "attrmap>=0.0.7",
+    "biopython>=1.8.1",
+    "pandas",
+    "matplotlib",
+    "snakemake-executor-plugin-slurm>=0.5.1"
+]
+
+[project.scripts]
+mitobee = "mitobee.__main__:main"
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["mitobee*"]
+
+# Configure setuptools_scm (reads version from your Git tags)
+[tool.setuptools_scm]
+write_to = "mitobee/_version.py"
+fallback_version = "0.1.0"
+version_scheme = "post-release"
+local_scheme = "no-local-version"

mitobee-1.0.post0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+