GPatch 0.3.0__tar.gz

GPatch-0.3.0/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at adadiehl@umich.edu. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

GPatch-0.3.0/GPatch.egg-info/PKG-INFO

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+Metadata-Version: 2.1
+Name: GPatch
+Version: 0.3.0
+Summary: Assemble contigs into a chromosome-scalse pseudo-assembly using alignments to a reference sequence.
+Home-page: https://github.com/adadiehl/GPatch
+Author: Adam Diehl
+Author-email: adadiehl@umich.edu
+License: UNKNOWN
+Description: # GPatch
+        ## Assemble contigs into a chromosome-scalse pseudo-assembly using alignments to a reference sequence.
+        
+        Starting with alignments of contigs to a reference genome, produce a chromosome-scale pseudoassembly by patching gaps between mapped contigs with sequences from the reference.
+        
+        ## Dependencies
+        * Python >= v3.7
+        * samtools (https://github.com/samtools/samtools)
+        * biopython (https://biopython.org/)
+        * pysam (https://github.com/pysam-developers/pysam)
+        * minimap2 (https://github.com/lh3/minimap2)
+        
+        We recommend using minimap2 for alignment, using the -a option to generate SAM output.
+        
+        ## Installation
+        
+        We recommend installing with conda, into a new environment:
+        ```
+        conda create -n GPatch -c conda-forge -c bioconda Bio pysam minimap2 samtools GPatch
+        ```
+        
+        Install with pip:
+        ```
+        pip install GPatch
+        ```
+        
+        Installation from the github repository is not recommended. However, if you must, follow the steps below:
+        1) git clone https://github.com/adadiehl/GPatch
+        2) cd GPatch/
+        3) python3 -m pip install -e .
+        
+        
+        ## Usage
+        ```
+        usage: GPatch [-h] -q SAM/BAM -r FASTA [-x BED] [-b FILENAME] [-m N]
+                               [-d N] [-f FLOAT] [-e FLOAT]
+        ```
+        
+        Starting with alignments of contigs to a reference genome, produce a chromosome-scale pseudoassembly by patching gaps between mapped contigs with sequences from the reference. Reference chromosomes with no mapped contigs are printed to output unchanged.
+        
+        #### Required Arguments
+        | Argument | Description |
+        |---|---|
+        | __-q SAM/BAM, --query_bam SAM/BAM__ | Path to SAM/BAM file containing non-overlapping contig mappings to the reference genome. |
+        | __-r FASTA, --reference_fasta FASTA__ | Path to reference genome fasta. |
+        
+        #### Optional Arguments:
+        | Argument | Description |
+        |---|---|
+        | __-h, --help__ | Show this help message and exit. |
+        | __-x STR, --prefix STR__ | Prefix to add to output file names. Default=None |
+        | __-b FILENAME, --store_final_bam FILENAME__ | Store the final set of primary contig alignments to the given file name. Default: Do not store the final BAM. |
+        | __-m N, --min_qual_score N__ | Minimum mapping quality score to retain an alignment. Default=30 |
+        
+        
+        ## Output
+        
+        GPatch produces three output files:
+        | File | Description |
+        |---|---|
+        | __patched.fasta__ | The final patched genome. |
+        | __contigs.bed__ | Location of contigs in the coordinate frame of the patched genome. |
+        | __patches.bed__ | Location of patches in the coordinate frame of the reference genome. |
+        
+        
+        ## Citing GPatch
+        Please use the following citation if you use this software in your work:
+        
+        CITATION_HERE
+Keywords: genomics,genome assembly
+Platform: UNKNOWN
+Classifier: Development Status :: 4 - Beta
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Natural Language :: English
+Description-Content-Type: text/markdown

GPatch-0.3.0/GPatch.egg-info/SOURCES.txt

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+MANIFEST.in
+README.md
+pyproject.toml
+setup.py
+./CODE_OF_CONDUCT.md
+./LICENSE
+./requirements.txt
+GPatch.egg-info/PKG-INFO
+GPatch.egg-info/SOURCES.txt
+GPatch.egg-info/dependency_links.txt
+GPatch.egg-info/entry_points.txt
+GPatch.egg-info/not-zip-safe
+GPatch.egg-info/requires.txt
+GPatch.egg-info/top_level.txt

GPatch-0.3.0/GPatch.egg-info/dependency_links.txt

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+

GPatch-0.3.0/GPatch.egg-info/entry_points.txt

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+[console_scripts]
+GPatch.py = GPatch.GPatch:main
+

GPatch-0.3.0/GPatch.egg-info/not-zip-safe

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+

GPatch-0.3.0/GPatch.egg-info/requires.txt

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+Bio
+pysam

GPatch-0.3.0/GPatch.egg-info/top_level.txt

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+

GPatch-0.3.0/LICENSE

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+Copyright (c) 2018 Adam Diehl
+
+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.

GPatch-0.3.0/MANIFEST.in

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+include README.md
+include ./LICENSE
+include ./CODE_OF_CONDUCT.md
+include ./requirements.txt

GPatch-0.3.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: GPatch
+Version: 0.3.0
+Summary: Assemble contigs into a chromosome-scalse pseudo-assembly using alignments to a reference sequence.
+Home-page: https://github.com/adadiehl/GPatch
+Author: Adam Diehl
+Author-email: adadiehl@umich.edu
+License: UNKNOWN
+Description: # GPatch
+        ## Assemble contigs into a chromosome-scalse pseudo-assembly using alignments to a reference sequence.
+        
+        Starting with alignments of contigs to a reference genome, produce a chromosome-scale pseudoassembly by patching gaps between mapped contigs with sequences from the reference.
+        
+        ## Dependencies
+        * Python >= v3.7
+        * samtools (https://github.com/samtools/samtools)
+        * biopython (https://biopython.org/)
+        * pysam (https://github.com/pysam-developers/pysam)
+        * minimap2 (https://github.com/lh3/minimap2)
+        
+        We recommend using minimap2 for alignment, using the -a option to generate SAM output.
+        
+        ## Installation
+        
+        We recommend installing with conda, into a new environment:
+        ```
+        conda create -n GPatch -c conda-forge -c bioconda Bio pysam minimap2 samtools GPatch
+        ```
+        
+        Install with pip:
+        ```
+        pip install GPatch
+        ```
+        
+        Installation from the github repository is not recommended. However, if you must, follow the steps below:
+        1) git clone https://github.com/adadiehl/GPatch
+        2) cd GPatch/
+        3) python3 -m pip install -e .
+        
+        
+        ## Usage
+        ```
+        usage: GPatch [-h] -q SAM/BAM -r FASTA [-x BED] [-b FILENAME] [-m N]
+                               [-d N] [-f FLOAT] [-e FLOAT]
+        ```
+        
+        Starting with alignments of contigs to a reference genome, produce a chromosome-scale pseudoassembly by patching gaps between mapped contigs with sequences from the reference. Reference chromosomes with no mapped contigs are printed to output unchanged.
+        
+        #### Required Arguments
+        | Argument | Description |
+        |---|---|
+        | __-q SAM/BAM, --query_bam SAM/BAM__ | Path to SAM/BAM file containing non-overlapping contig mappings to the reference genome. |
+        | __-r FASTA, --reference_fasta FASTA__ | Path to reference genome fasta. |
+        
+        #### Optional Arguments:
+        | Argument | Description |
+        |---|---|
+        | __-h, --help__ | Show this help message and exit. |
+        | __-x STR, --prefix STR__ | Prefix to add to output file names. Default=None |
+        | __-b FILENAME, --store_final_bam FILENAME__ | Store the final set of primary contig alignments to the given file name. Default: Do not store the final BAM. |
+        | __-m N, --min_qual_score N__ | Minimum mapping quality score to retain an alignment. Default=30 |
+        
+        
+        ## Output
+        
+        GPatch produces three output files:
+        | File | Description |
+        |---|---|
+        | __patched.fasta__ | The final patched genome. |
+        | __contigs.bed__ | Location of contigs in the coordinate frame of the patched genome. |
+        | __patches.bed__ | Location of patches in the coordinate frame of the reference genome. |
+        
+        
+        ## Citing GPatch
+        Please use the following citation if you use this software in your work:
+        
+        CITATION_HERE
+Keywords: genomics,genome assembly
+Platform: UNKNOWN
+Classifier: Development Status :: 4 - Beta
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Natural Language :: English
+Description-Content-Type: text/markdown

GPatch-0.3.0/README.md

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+# GPatch
+## Assemble contigs into a chromosome-scalse pseudo-assembly using alignments to a reference sequence.
+
+Starting with alignments of contigs to a reference genome, produce a chromosome-scale pseudoassembly by patching gaps between mapped contigs with sequences from the reference.
+
+## Dependencies
+* Python >= v3.7
+* samtools (https://github.com/samtools/samtools)
+* biopython (https://biopython.org/)
+* pysam (https://github.com/pysam-developers/pysam)
+* minimap2 (https://github.com/lh3/minimap2)
+
+We recommend using minimap2 for alignment, using the -a option to generate SAM output.
+
+## Installation
+
+We recommend installing with conda, into a new environment:
+```
+conda create -n GPatch -c conda-forge -c bioconda Bio pysam minimap2 samtools GPatch
+```
+
+Install with pip:
+```
+pip install GPatch
+```
+
+Installation from the github repository is not recommended. However, if you must, follow the steps below:
+1) git clone https://github.com/adadiehl/GPatch
+2) cd GPatch/
+3) python3 -m pip install -e .
+
+
+## Usage
+```
+usage: GPatch [-h] -q SAM/BAM -r FASTA [-x BED] [-b FILENAME] [-m N]
+                       [-d N] [-f FLOAT] [-e FLOAT]
+```
+
+Starting with alignments of contigs to a reference genome, produce a chromosome-scale pseudoassembly by patching gaps between mapped contigs with sequences from the reference. Reference chromosomes with no mapped contigs are printed to output unchanged.
+
+#### Required Arguments
+| Argument | Description |
+|---|---|
+| __-q SAM/BAM, --query_bam SAM/BAM__ | Path to SAM/BAM file containing non-overlapping contig mappings to the reference genome. |
+| __-r FASTA, --reference_fasta FASTA__ | Path to reference genome fasta. |
+
+#### Optional Arguments:
+| Argument | Description |
+|---|---|
+| __-h, --help__ | Show this help message and exit. |
+| __-x STR, --prefix STR__ | Prefix to add to output file names. Default=None |
+| __-b FILENAME, --store_final_bam FILENAME__ | Store the final set of primary contig alignments to the given file name. Default: Do not store the final BAM. |
+| __-m N, --min_qual_score N__ | Minimum mapping quality score to retain an alignment. Default=30 |
+
+
+## Output
+
+GPatch produces three output files:
+| File | Description |
+|---|---|
+| __patched.fasta__ | The final patched genome. |
+| __contigs.bed__ | Location of contigs in the coordinate frame of the patched genome. |
+| __patches.bed__ | Location of patches in the coordinate frame of the reference genome. |
+
+
+## Citing GPatch
+Please use the following citation if you use this software in your work:
+
+CITATION_HERE

GPatch-0.3.0/pyproject.toml

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+[build-system]
+requires= ['setuptools', 'wheel', 'Bio', 'pysam', 'samtools']

GPatch-0.3.0/requirements.txt

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+Bio
+pysam

GPatch-0.3.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

GPatch-0.3.0/setup.py

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+import sys
+
+if sys.version_info > (3, ) and sys.version_info < (3, 7):
+    sys.exit("ERROR: GPatch requires Python 3.7 or greater")
+
+try:
+    from setuptools import setup, find_packages
+except ImportError:
+    from ez_setup import use_setuptools
+    use_setuptools()
+
+from setuptools import setup, find_packages
+from pathlib import Path
+from glob import glob
+
+def readme():
+    if sys.version_info > (3, ):
+        with open(Path(__file__).parent.resolve() / 'README.md', encoding='utf-8') as md:
+            return md.read()
+    else:
+        with open('README.md') as md:
+            return md.read()
+
+def main():
+
+    metadata = dict(
+        name="GPatch",
+        version="0.3.0",
+        author="Adam Diehl",
+        author_email="adadiehl@umich.edu",
+        description="Assemble contigs into a chromosome-scalse pseudo-assembly using alignments to a reference sequence.",
+        long_description=readme(),
+        long_description_content_type="text/markdown",
+        url="https://github.com/adadiehl/GPatch",
+        packages = find_packages(),
+        package_data = {
+            'GPatch': [
+                "LICENSE",
+                "CODE_OF_CONDUCT.md"
+            ]
+        },
+        setup_requires=[
+            'Bio',
+            'pysam'
+        ],
+        install_requires=[
+            'Bio',
+            'pysam'
+        ],
+        entry_points={
+            'console_scripts': [
+                'GPatch.py = GPatch.GPatch:main'
+            ]
+        },
+        classifiers=[
+            "Development Status :: 4 - Beta",
+            "Programming Language :: Python :: 3",
+            "License :: OSI Approved :: MIT License",
+            "Operating System :: OS Independent",
+            "Intended Audience :: Science/Research",
+            "Topic :: Scientific/Engineering",
+            "Topic :: Scientific/Engineering :: Information Analysis",
+            "Natural Language :: English"
+        ],
+        keywords = "genomics, genome assembly",
+        include_package_data=True,
+        zip_safe=False,
+    )
+            
+    setup(**metadata)
+        
+if __name__ == "__main__":
+    main()