feat: Rseqc inner distance #3140
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* perf: update bio/bcftools/index/environment.yaml. * perf: update bio/bcftools/index/environment.yaml. * perf: update bio/bcftools/index/environment.yaml.
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* Add autobump action * fix paths * dbg * dbg branch * add checkout * dbg * trigger rerun * entity regex and add label * dbg * Update autobump.yml * Update autobump.yml
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WalkthroughThis update introduces several new files related to the Changes
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| aln="A.bam", | ||
| refgene="annotation.bed", | ||
| output: | ||
| txt="a.txt", |
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Maybe use a more specific name than txt. What does this file contain?
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It's a trash-file IMO. I don't know any tool that uses this file (multiqc uses the output.freq file, both PDF and R scripts are used by us, humans). RSeQC itself never reads the content of this file.
This file is a TSV is not described by any official documentation. I just read the code, and, for each read in the input (bam/sam), it contains the following: read name <tab> inner_distance if no filtered else NA <tab> comments about read pair.
Let's call it reads_inner_distance ?
Co-authored-by: Filipe G. Vieira <[email protected]>
Co-authored-by: Filipe G. Vieira <[email protected]>
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Actionable comments posted: 0
Outside diff range, codebase verification and nitpick comments (1)
test.py (1)
6478-6482: Consider Adding Generic Exception Handling inrunFunctionThe
runfunction currently handles specific conditions with custom exceptions but lacks a broader exception handling mechanism. Consider adding generic exception handling to catch and log unexpected errors to improve robustness.
- Review the
runfunction to ensure all potential error cases are covered.Analysis chain
LGTM! Verify error handling in the
runfunction.The function is correctly implemented. Ensure that the
runfunction handles exceptions correctly and logs any errors.The code changes are approved.
Run the following script to verify the error handling in the
runfunction:Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify error handling in the `run` function. # Test: Search for exception handling in the `run` function. Expect: Proper logging of errors. rg --type python -A 5 'def run' | grep -A 5 'except Exception as e'Length of output: 100
Script:
#!/bin/bash # Description: Verify error handling in the `run` function. # Test: Search for exception handling in the `run` function. Expect: Proper logging of errors. rg --type py -A 10 'def run' | grep -A 10 'except Exception as e'Length of output: 67
Script:
#!/bin/bash # Description: Search for the `run` function and inspect its implementation for error handling. # Test: Search for the `run` function definition and its complete implementation. rg --type py -A 50 'def run'Length of output: 2345
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Files selected for processing (7)
- bio/rseqc/inner_distance/environment.linux-64.pin.txt (1 hunks)
- bio/rseqc/inner_distance/environment.yaml (1 hunks)
- bio/rseqc/inner_distance/meta.yaml (1 hunks)
- bio/rseqc/inner_distance/test/Snakefile (1 hunks)
- bio/rseqc/inner_distance/test/annotation.bed (1 hunks)
- bio/rseqc/inner_distance/wrapper.py (1 hunks)
- test.py (1 hunks)
Files skipped from review due to trivial changes (2)
- bio/rseqc/inner_distance/environment.linux-64.pin.txt
- bio/rseqc/inner_distance/environment.yaml
Additional context used
Path-based instructions (2)
bio/rseqc/inner_distance/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 theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.
Pattern
**/wrapper.py: Do not complain about use of undefined variable calledsnakemake.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 theselfargument of methods.
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Additional comments not posted (19)
bio/rseqc/inner_distance/test/annotation.bed (1)
1-2: LGTM!The BED file is correctly formatted.
The code changes are approved.
bio/rseqc/inner_distance/test/Snakefile (6)
1-1: LGTM!The rule name is descriptive and follows naming conventions.
The code changes are approved.
2-4: LGTM!The input files are correctly specified and relevant to the task.
The code changes are approved.
5-9: LGTM!The output files are correctly specified and relevant to the task. The file names are descriptive.
The code changes are approved.
10-11: LGTM!The log file is correctly specified and relevant to the task.
The code changes are approved.
12-13: LGTM!The extra parameters are correctly specified and relevant to the task.
The code changes are approved.
14-15: LGTM!The wrapper path is correctly specified and relevant to the task.
The code changes are approved.
bio/rseqc/inner_distance/meta.yaml (5)
1-2: LGTM!The name and description are correctly specified and relevant to the task.
The code changes are approved.
3-5: LGTM!The URL and authors are correctly specified and relevant to the task.
The code changes are approved.
6-8: LGTM!The input files are correctly specified and relevant to the task.
The code changes are approved.
9-13: LGTM!The output files are correctly specified and relevant to the task.
The code changes are approved.
14-15: LGTM!The extra parameters are correctly specified and relevant to the task.
The code changes are approved.
bio/rseqc/inner_distance/wrapper.py (7)
1-9: LGTM!The file encoding, docstring, and author information are correctly implemented.
The code changes are approved.
10-12: LGTM!The import statements are correctly implemented and necessary for the functionality.
The code changes are approved.
13-15: Address log overwriting concern.The
logvariable usesappend=True, which should prevent overwriting. However, ensure that this behavior is as expected.Please verify that the logs are appended and not overwritten.
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16-23: LGTM!The shell command execution within a temporary directory is correctly implemented.
The code changes are approved.
25-31: LGTM!The conditional block for moving the
reads_inner_distanceoutput file is correctly implemented.The code changes are approved.
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32-37: LGTM!The conditional block for moving the
The code changes are approved.
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39-51: LGTM!The conditional blocks for moving the
freqandplot_routput files are correctly implemented.The code changes are approved.
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Actionable comments posted: 0
Review details
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Files selected for processing (7)
- bio/rseqc/inner_distance/environment.linux-64.pin.txt (1 hunks)
- bio/rseqc/inner_distance/environment.yaml (1 hunks)
- bio/rseqc/inner_distance/meta.yaml (1 hunks)
- bio/rseqc/inner_distance/test/Snakefile (1 hunks)
- bio/rseqc/inner_distance/test/annotation.bed (1 hunks)
- bio/rseqc/inner_distance/wrapper.py (1 hunks)
- test.py (1 hunks)
Files skipped from review due to trivial changes (3)
- bio/rseqc/inner_distance/environment.linux-64.pin.txt
- bio/rseqc/inner_distance/environment.yaml
- bio/rseqc/inner_distance/test/annotation.bed
Additional context used
Path-based instructions (2)
bio/rseqc/inner_distance/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 theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.
Pattern
**/wrapper.py: Do not complain about use of undefined variable calledsnakemake.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 theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.
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Additional comments not posted (16)
bio/rseqc/inner_distance/test/Snakefile (5)
2-4: LGTM!The input section is correctly defined.
The code changes are approved.
5-9: LGTM!The output section is correctly defined.
The code changes are approved.
10-11: LGTM!The log section is correctly defined.
The code changes are approved.
12-13: LGTM!The params section is correctly defined.
The code changes are approved.
14-15: LGTM!The wrapper section is correctly defined.
The code changes are approved.
bio/rseqc/inner_distance/meta.yaml (5)
1-2: LGTM!The name and description section is correctly defined.
The code changes are approved.
3-3: LGTM!The url section is correctly defined.
The code changes are approved.
4-5: LGTM!The authors section is correctly defined.
The code changes are approved.
6-8: LGTM!The input section is correctly defined.
The code changes are approved.
9-15: LGTM!The output and params sections are correctly defined.
The code changes are approved.
bio/rseqc/inner_distance/wrapper.py (5)
3-8: LGTM!The metadata section is correctly defined.
The code changes are approved.
10-11: LGTM!The imports section is correctly defined.
The code changes are approved.
13-14: LGTM!The extra and log parameters section is correctly defined.
The code changes are approved.
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16-23: LGTM!The main shell command section is correctly defined.
The code changes are approved.
25-51: LGTM!The output handling section is correctly defined.
The code changes are approved.
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test.py (1)
6491-6496: LGTM!The function is correctly implemented and follows the pattern used in other test functions.
The code changes are approved.
🤖 I have created a release \*beep\* \*boop\* --- ## [4.3.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.2.0...v4.3.0) (2024-08-28) ### Features * add support for multiple input file subcommands in seqkit wrapper (subcommands "common" and "concat") ([#3142](https://www.github.com/snakemake/snakemake-wrappers/issues/3142)) ([3b5391f](https://www.github.com/snakemake/snakemake-wrappers/commit/3b5391f619b38334829c06b8bd0526a16e19c732)) * Deeptools multibigwig summary ([#3135](https://www.github.com/snakemake/snakemake-wrappers/issues/3135)) ([df7e2bf](https://www.github.com/snakemake/snakemake-wrappers/commit/df7e2bffdd61690e56380bb1b49ca663e58a477c)) * Deeptools plot correlation ([#3137](https://www.github.com/snakemake/snakemake-wrappers/issues/3137)) ([a965bd6](https://www.github.com/snakemake/snakemake-wrappers/commit/a965bd62f13bb62722daf08201a00b1f26bef38d)) * Deeptools plot pca ([#3138](https://www.github.com/snakemake/snakemake-wrappers/issues/3138)) ([0d9862b](https://www.github.com/snakemake/snakemake-wrappers/commit/0d9862b0f91e74bb90993eb7ecb938dec80d779b)) * Rseqc bamstat ([#3139](https://www.github.com/snakemake/snakemake-wrappers/issues/3139)) ([b4267e6](https://www.github.com/snakemake/snakemake-wrappers/commit/b4267e6a0244071a96efc8a91fd6ba982a738cb5)) * Rseqc inner distance ([#3140](https://www.github.com/snakemake/snakemake-wrappers/issues/3140)) ([8ca10f3](https://www.github.com/snakemake/snakemake-wrappers/commit/8ca10f3949ca6fb1ed9f9d046c89ca10a7c32c8c)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
QC
snakemake-wrappers.While the contributions guidelines are more extensive, please particularly ensure that:
test.pywas updated to call any added or updated example rules in aSnakefileinput:andoutput:file paths in the rules can be chosen arbitrarilyinput:oroutput:)tempfile.gettempdir()points tometa.yamlcontains a link to the documentation of the respective tool or command underurl:Summary by CodeRabbit
New Features
environment.linux-64.pin.txtfor a reproducible Conda environment setup on Linux 64-bit.environment.yamlto streamline the installation of therseqcpackage and its dependencies.inner_distancetool to calculate inner distances between read pairs in genomic data.annotation.bedfile for genomic feature representation.Enhancements
Tests