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<!-- Ensure that the PR title follows conventional commit style (<type>: <description>)--> <!-- Possible types are here: https://github.com/commitizen/conventional-commit-types/blob/master/index.json --> <!-- Add a description of your PR here--> ### QC <!-- Make sure that you can tick the boxes below. --> * [x] I confirm that I have followed the [documentation for contributing to `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html). While the contributions guidelines are more extensive, please particularly ensure that: * [x] `test.py` was updated to call any added or updated example rules in a `Snakefile` * [x] `input:` and `output:` file paths in the rules can be chosen arbitrarily * [x] wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`) * [x] 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 * [x] the `meta.yaml` contains a link to the documentation of the respective tool or command under `url:` * [x] conda environments use a minimal amount of channels and packages, in recommended ordering <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Introduced `environment.linux-64.pin.txt` for a reproducible Conda environment setup on Linux 64-bit. - Added `environment.yaml` to streamline the installation of the `rseqc` package and its dependencies. - Launched the `inner_distance` tool to calculate inner distances between read pairs in genomic data. - Implemented a structured `annotation.bed` file for genomic feature representation. - **Enhancements** - Added a Snakemake rule for analyzing inner distances in RNA sequencing data. - Created a wrapper to facilitate the integration of the inner distance functionality into Snakemake workflows. - **Tests** - Included a new test case for the inner distance calculation process within the bioinformatics toolkit. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: tdayris <[email protected]> Co-authored-by: tdayris <[email protected]> Co-authored-by: Johannes Köster <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Co-authored-by: Felix Mölder <[email protected]> Co-authored-by: Christopher Schröder <[email protected]> Co-authored-by: Filipe G. Vieira <[email protected]>
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| # This file may be used to create an environment using: | ||
| # $ conda create --name <env> --file <this file> | ||
| # platform: linux-64 | ||
| @EXPLICIT | ||
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| https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef | ||
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| https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 | ||
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| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - nodefaults | ||
| dependencies: | ||
| - rseqc=5.0.3 |
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| name: inner_distance | ||
| description: Calculate inner distance between read pairs | ||
| url: "https://rseqc.sourceforge.net/#inner-distance-py" | ||
| authors: | ||
| - "Thibault Dayris" | ||
| input: | ||
| - aln: Path to SAM/BAM input | ||
| - refgene: Path to refgene model | ||
| output: | ||
| - reads_inner_distance: Optional path to per-read inner distance table | ||
| - pdf: Optional path to pdf graph | ||
| - plot_r: Optional Path to R script | ||
| - freq: Optional path to inner distance frequence | ||
| params: | ||
| - extra: Optional parameters for `inner_distance.py`, besides `-i`, `-r`, or `-o` |
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| rule test_rseqc_inner_distance: | ||
| input: | ||
| aln="A.bam", | ||
| refgene="annotation.bed", | ||
| output: | ||
| reads_inner_distance="a.txt", | ||
| freq="freq.txt", | ||
| pdf="a.pdf", | ||
| plot_r="script.a.r", | ||
| log: | ||
| "rseqc.log", | ||
| params: | ||
| extra="-k3 -q2", | ||
| wrapper: | ||
| "master/bio/rseqc/inner_distance" |
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| 1 0 80 ENST00000000000 0 + 80 80 0 1 80, 0, | ||
| 2 0 80 ENST00000000001 0 + 80 80 0 1 80, 0, |
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| # coding: utf-8 | ||
|
|
||
| """Snakemake wrapper for RSeQC inner_distance.py""" | ||
|
|
||
| __author__ = "Thibault Dayris" | ||
| __mail__ = "[email protected]" | ||
| __copyright__ = "Copyright 2024, Thibault Dayris" | ||
| __license__ = "MIT" | ||
|
|
||
| from tempfile import TemporaryDirectory | ||
| from snakemake import shell | ||
|
|
||
| extra = snakemake.params.get("extra", "") | ||
| log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True) | ||
|
|
||
| with TemporaryDirectory() as tempdir: | ||
| shell( | ||
| "inner_distance.py {extra} " | ||
| "--input-file {snakemake.input.aln} " | ||
| "--refgene {snakemake.input.refgene} " | ||
| "--out-prefix {tempdir}/out " | ||
| "{log} " | ||
| ) | ||
|
|
||
| if snakemake.output.get("reads_inner_distance"): | ||
| shell( | ||
| "mv --verbose " | ||
| "{tempdir}/out.inner_distance.txt " | ||
| "{snakemake.output.reads_inner_distance} {log}" | ||
| ) | ||
|
|
||
| if snakemake.output.get("pdf"): | ||
| shell( | ||
| "mv --verbose " | ||
| "{tempdir}/out.inner_distance_plot.pdf " | ||
| "{snakemake.output.pdf} {log}" | ||
| ) | ||
|
|
||
| if snakemake.output.get("freq"): | ||
| shell( | ||
| "mv --verbose " | ||
| "{tempdir}/out.inner_distance_freq.txt " | ||
| "{snakemake.output.freq} {log}" | ||
| ) | ||
|
|
||
| if snakemake.output.get("plot_r"): | ||
| shell( | ||
| "mv --verbose " | ||
| "{tempdir}/out.inner_distance_plot.r " | ||
| "{snakemake.output.plot_r} {log}" | ||
| ) |
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