feat: Rseqc bamstat

[tdayris]

QC

• I confirm that I have followed the documentation for contributing to snakemake-wrappers.

While the contributions guidelines are more extensive, please particularly ensure that:

• test.py was updated to call any added or updated example rules in a Snakefile
• input: and output: file paths in the rules can be chosen arbitrarily
• wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:)
• temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to
• the meta.yaml contains a link to the documentation of the respective tool or command under url:
• conda environments use a minimal amount of channels and packages, in recommended ordering

Summary by CodeRabbit

• New Features

  • Introduced a comprehensive Conda environment configuration for the rseqc package to facilitate reproducible bioinformatics workflows.
  • Added a new tool for summarizing mapping statistics from BAM/SAM files, complete with metadata and functionality descriptions.
  • Implemented a Snakemake rule for processing BAM files, enhancing the integration of BAM analysis into workflows.
  • Created a wrapper script for executing the BAM statistics tool within Snakemake.

• Tests

  • Added a new test function to improve testing coverage for the bio/rseqc functionality related to BAM statistics.

[coderabbitai]

Walkthrough

The changes introduce new files and configurations for the RSeQC package, specifically the bam_stat tool. This includes a Conda environment specification, metadata for the tool, a Snakemake rule for BAM file processing, and a wrapper script to integrate the tool into Snakemake workflows. Additionally, a test function for the BAM statistics functionality has been added to ensure coverage within the testing framework.

Changes

Files	Change Summary
bio/rseqc/bam_stat/environment.linux-64.pin.txt, bio/rseqc/bam_stat/environment.yaml	New files created to specify package dependencies and environment configuration for the rseqc package, ensuring reproducibility and accessibility of required tools and libraries.
bio/rseqc/bam_stat/meta.yaml	New file created to provide metadata for the bam_stat.py tool, including its name, URL, description, authorship, input/output specifications, and parameters.
bio/rseqc/bam_stat/test/Snakefile	New Snakemake rule added to facilitate BAM file processing, specifying input/output files, parameters, and logging.
bio/rseqc/bam_stat/wrapper.py	New wrapper script introduced to execute the bam_stat.py script within a Snakemake workflow, capturing logs and handling parameters.
test.py	New test function added to validate the functionality of the bio/rseqc/bam_stat module, ensuring integration with the existing testing framework without altering previous tests.

---

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[coderabbitai]

Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between a965bd6 and f4c7bbf.

Files selected for processing (6)

• bio/rseqc/bam_stat/environment.linux-64.pin.txt (1 hunks)
• bio/rseqc/bam_stat/environment.yaml (1 hunks)
• bio/rseqc/bam_stat/meta.yaml (1 hunks)
• bio/rseqc/bam_stat/test/Snakefile (1 hunks)
• bio/rseqc/bam_stat/wrapper.py (1 hunks)
• test.py (1 hunks)

Files skipped from review due to trivial changes (2)

• bio/rseqc/bam_stat/environment.linux-64.pin.txt
• bio/rseqc/bam_stat/environment.yaml

Additional context used

Path-based instructions (2)

bio/rseqc/bam_stat/wrapper.py (2)

Pattern **/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

---

Pattern **/wrapper.py: Do not complain about use of undefined variable called snakemake.

test.py (1)

Pattern **/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

Ruff

bio/rseqc/bam_stat/wrapper.py

10-10: Undefined name snakemake

(F821)

---

11-11: Undefined name snakemake

(F821)

Additional comments not posted (20)

bio/rseqc/bam_stat/test/Snakefile (6)

1-12: Ensure input file exists.

Verify that the input file a.bam exists and is correctly referenced.

---

4-5: Ensure output file path is correct.

Verify that the output file path a.stats is correctly referenced.

---

6-6: Threads specification is appropriate.

The rule specifies a single thread, which is appropriate for this task.

---

8-8: Parameter specification is appropriate.

The extra parameter is correctly specified with --mapq 5.

---

10-10: Log file path is appropriate.

The log file path bastat.log is correctly specified.

---

12-12: Wrapper path is appropriate.

The wrapper path master/bio/rseqc/bam_stat is correctly specified.

bio/rseqc/bam_stat/wrapper.py (5)

1-6: Metadata is appropriate.

The metadata section is correctly specified with author, mail, copyright, and license information.

---

8-8: Import statement is appropriate.

The import statement for shell from snakemake is correctly specified.

---

10-10: Parameter retrieval is appropriate.

The extra parameter is correctly retrieved using snakemake.params.get.

Tools

Ruff

10-10: Undefined name snakemake

(F821)

---

11-11: Log formatting is appropriate.

The log is correctly formatted using snakemake.log_fmt_shell.

Tools

Ruff

11-11: Undefined name snakemake

(F821)

---

13-13: Shell command execution is appropriate.

The shell command is correctly executed using the shell function. However, ensure that snakemake is defined in the context where this script is executed.

bio/rseqc/bam_stat/meta.yaml (8)

1-1: Name is appropriate.

The name RSeQC bam_stat.py is correctly specified.

---

2-2: URL is appropriate.

The URL https://rseqc.sourceforge.net/#bam-stat-py is correctly specified.

---

3-4: Description is appropriate.

The description Summarizing mapping statistics of a BAM or SAM file. is correctly specified.

---

5-6: Authors are appropriate.

The author Thibault Dayris is correctly specified.

---

7-8: Input is appropriate.

The input Path to BAM/SAM file(s) to summarize. is correctly specified.

---

9-10: Output is appropriate.

The output Path to summary is correctly specified.

---

11-12: Params are appropriate.

The params extra: Optional argument besides --input-file are correctly specified.

---

13-14: Notes are appropriate.

The notes Only mapping quality can be provided as optional parameters, since --help and --version do not produce summary. are correctly specified.

test.py (1)

6444-6448: LGTM! Verify error handling in the run function.

The function is correctly implemented. Ensure that the run function handles errors appropriately to make the test meaningful.

Run the following script to verify the error handling in the run function:

[coderabbitai]

Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between f4c7bbf and 54a838d.

Files selected for processing (1)

• test.py (1 hunks)

Files skipped from review as they are similar to previous changes (1)

• test.py

[coderabbitai]

Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 54a838d and b15bccc.

Files selected for processing (1)

• test.py (1 hunks)

Files skipped from review as they are similar to previous changes (1)

• test.py