Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Translate summarize_counts.R #110

Closed
Tracked by #107
ns-rse opened this issue Dec 12, 2024 · 0 comments · Fixed by #121
Closed
Tracked by #107

Translate summarize_counts.R #110

ns-rse opened this issue Dec 12, 2024 · 0 comments · Fixed by #121
Labels
r to python

Comments

@ns-rse
Copy link
Contributor

ns-rse commented Dec 12, 2024 •
edited
Loading

See
summarize_counts.R
@ns-rse ns-rse mentioned this issue Dec 12, 2024
Open
10 tasks
ns-rse added a commit that referenced this issue Dec 13, 2024
@ns-rse
feature(summary_counts): Translates R code to Python
cfd1df0 
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.
@ns-rse ns-rse mentioned this issue Dec 13, 2024
Merged
ns-rse added a commit that referenced this issue Dec 13, 2024
@ns-rse
feature(summary_counts): Translates R code to Python
6219ac6 
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.
@ns-rse ns-rse closed this as completed in f0520ad Dec 13, 2024
@ns-rse ns-rse mentioned this issue Jan 30, 2025
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
r to python
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

feature(summary_counts): Translates R code to Python sudlab/IsoSLAM
1 participant
@ns-rse