GPatch 0.3.0__py3-none-any.whl
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Copyright (c) 2018 Adam Diehl
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Metadata-Version: 2.1
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Name: GPatch
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Version: 0.3.0
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Summary: Assemble contigs into a chromosome-scalse pseudo-assembly using alignments to a reference sequence.
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Home-page: https://github.com/adadiehl/GPatch
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Author: Adam Diehl
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Author-email: adadiehl@umich.edu
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License: UNKNOWN
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Keywords: genomics,genome assembly
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Platform: UNKNOWN
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Classifier: Development Status :: 4 - Beta
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Classifier: Programming Language :: Python :: 3
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Operating System :: OS Independent
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Classifier: Intended Audience :: Science/Research
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Classifier: Topic :: Scientific/Engineering
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Classifier: Topic :: Scientific/Engineering :: Information Analysis
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Classifier: Natural Language :: English
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Description-Content-Type: text/markdown
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Requires-Dist: Bio
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Requires-Dist: pysam
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# GPatch
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## Assemble contigs into a chromosome-scalse pseudo-assembly using alignments to a reference sequence.
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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.
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## Dependencies
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* Python >= v3.7
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* samtools (https://github.com/samtools/samtools)
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* biopython (https://biopython.org/)
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* pysam (https://github.com/pysam-developers/pysam)
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* minimap2 (https://github.com/lh3/minimap2)
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We recommend using minimap2 for alignment, using the -a option to generate SAM output.
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## Installation
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We recommend installing with conda, into a new environment:
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```
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conda create -n GPatch -c conda-forge -c bioconda Bio pysam minimap2 samtools GPatch
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```
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Install with pip:
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```
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pip install GPatch
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```
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Installation from the github repository is not recommended. However, if you must, follow the steps below:
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1) git clone https://github.com/adadiehl/GPatch
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2) cd GPatch/
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3) python3 -m pip install -e .
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## Usage
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```
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usage: GPatch [-h] -q SAM/BAM -r FASTA [-x BED] [-b FILENAME] [-m N]
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[-d N] [-f FLOAT] [-e FLOAT]
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```
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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.
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#### Required Arguments
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| Argument | Description |
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|---|---|
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| __-q SAM/BAM, --query_bam SAM/BAM__ | Path to SAM/BAM file containing non-overlapping contig mappings to the reference genome. |
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| __-r FASTA, --reference_fasta FASTA__ | Path to reference genome fasta. |
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#### Optional Arguments:
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| Argument | Description |
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|---|---|
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| __-h, --help__ | Show this help message and exit. |
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| __-x STR, --prefix STR__ | Prefix to add to output file names. Default=None |
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| __-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. |
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| __-m N, --min_qual_score N__ | Minimum mapping quality score to retain an alignment. Default=30 |
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## Output
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GPatch produces three output files:
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| File | Description |
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|---|---|
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| __patched.fasta__ | The final patched genome. |
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| __contigs.bed__ | Location of contigs in the coordinate frame of the patched genome. |
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| __patches.bed__ | Location of patches in the coordinate frame of the reference genome. |
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## Citing GPatch
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Please use the following citation if you use this software in your work:
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CITATION_HERE
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GPatch-0.3.0.dist-info/LICENSE,sha256=7BlC-5xXMV3VWITTxG48u7CXTMZH51XX_i7A_WQofTM,1054
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GPatch-0.3.0.dist-info/METADATA,sha256=OL2qAI8zVk-N_VeRPB4DL4dMIPNt65ljs33RrMrel98,3352
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GPatch-0.3.0.dist-info/WHEEL,sha256=OqRkF0eY5GHssMorFjlbTIq072vpHpF60fIQA6lS9xA,92
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GPatch-0.3.0.dist-info/entry_points.txt,sha256=Ghl6CN8E-Io-lpCVUtV8zdetHk6wYTZ01MLx7eC2t6k,50
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GPatch-0.3.0.dist-info/top_level.txt,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
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GPatch-0.3.0.dist-info/RECORD,,
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