feature(summary_counts): Translates R code to Python #121
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Closes #110 - Updates `isoslam/default_config.yaml` and `processing` argparse to be consistent. - In turn the `utils.update_config()` function has been corrected with additional tests to correctly update nested dictionaries from the configuration. - Logging is setup and `loguru` used with formatted output and level set from configuration or command line optoins. - Translates the R code that counted and summarised the transcripts to Python code (using Pandas) along with tests. - Necessary updates to `pyproject.toml`. The output from IsoSLAM can now be summarised using... ```bash isoslam --output-dir output summary-counts --file-pattern "tests/**/*.tsv" ``` Rather than calling `Rscript` to do the work. This will serve as a template for translating the other R code.
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Closes #110
Adds the sub-command
isoslam summary-counts. Required a fair bit of work being the first processor that loads and usesthe configuration file.
isoslam --config, otherwise loads theconfiguration and uses that.
isoslam/default_config.yamlandisoslam/processing.pyso that argparse values are consistent.utils.update_config()function has been corrected with additional tests to correctly update nesteddictionaries from the configuration. Command line options over-ride those in any configuration file.
loguruused with formatted output and level set from configuration or command line optoins.pyproject.toml.The output from IsoSLAM can now be summarised using...
...rather than calling
Rscript pipeline_slam_3UIs <dir> <regex> <outfile>to do the work.This will serve as a template for translating the other R code.