Update MAG class to MetaBin #67
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* resolves issue-KwanLab#54 * 📝 Update docstrings missing for functions. * 🐎 Add cache for properties reading assembly sequences. * 🎨 Add Entrypoint functionality for incorporation to packaging/distribution. * 🎨🐛 Update main() to handle updated functions.
* 📝 Add docstrings to methods and class * 🎨🔥 Remove split_nucleotides method. * 🎨 Update get_binning function to handle coverages as filepath not pd.DataFrame * 🎨 Change mag.py to metabin.py * 🐎 fixed from PR-KwanLab#66. Add cache functionality to time-consuming property methods. * 📝 Add COMBAK comment for checkpointing. Return to this when implemented in utilities.py
evanroyrees
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jason-c-kwan
reviewed
May 7, 2020
autometa/common/metabin.py
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| f'Num. Nucl. ORFs: {self.nnucls:,}\n' | ||
| f'Num. Prot. ORFs: {self.nprots:,}\n' | ||
| f'Size: {self.size:,}bp / {self.totalsize:,}bp ({self.size_pct:4.2f}% of total metagenome)\n' | ||
| f'Mean GC content: {self.length_weighted_gc:4.2f}%\n' |
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The print output should probably explicitly say the GC content is length-weighted.
jason-c-kwan
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May 7, 2020
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I think I just had one comment. I like the docstrings for properties in metabin.py. For consistency it would be good to have them in metagenome.py, either as part of this PR or PR #66.
* 📝🎨 Add defaults formatter_class to template.py
* 🎨 Change os.stat(fpath).st_size to os.path.getsize(fpath)
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I recommend addressing #66 prior to this. |
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The comment above about the |
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This was addressed in commit 3033b0d The changes should be reflected in the |
jason-c-kwan
approved these changes
May 14, 2020
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user.pyforget_binningrather thanpd.DataFrame.mag.pytometabin.py.utilities.py.