feat: Rseqc inner distance

bio/rseqc/inner_distance/environment.linux-64.pin.txt

@@ -0,0 +1,107 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
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bio/rseqc/inner_distance/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - rseqc=5.0.3

bio/rseqc/inner_distance/meta.yaml

@@ -0,0 +1,15 @@
+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`

bio/rseqc/inner_distance/test/Snakefile

@@ -0,0 +1,15 @@
+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"

bio/rseqc/inner_distance/test/annotation.bed

@@ -0,0 +1,2 @@
+1	0	80	ENST00000000000	0	+	80	80	0	1	80,	0,
+2	0	80	ENST00000000001	0	+	80	80	0	1	80,	0,

bio/rseqc/inner_distance/wrapper.py

@@ -0,0 +1,51 @@
+# 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}"
+        )

test.py

@@ -6488,6 +6488,14 @@ def test_generate_data_matrix():
     )
 
 
+@skip_if_not_modified
+def test_rseqc_inner_distance():
+    run(
+        "bio/rseqc/inner_distance",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "a.pdf"],
+    )
+
+
 @skip_if_not_modified
 def test_rseqc_infer_experiment():
     run(