From aa43543e1fb609901d09b7a9f0c5e72707cb47a4 Mon Sep 17 00:00:00 2001
From: Emma Rousseau <emmarou1@icloud.com>
Date: Sat, 26 Oct 2024 20:42:22 +0200
Subject: [PATCH] Rseqc innerdistance (#159)

* initial commit dedup

* Revert "initial commit dedup"

This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.

* full component with two tests

* fix default values

* adjust argument names and container image

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
---
 CHANGELOG.md                                  |   1 +
 .../rseqc_inner_distance/config.vsh.yaml      | 116 ++++++++++++++++++
 src/rseqc/rseqc_inner_distance/help.txt       |  43 +++++++
 src/rseqc/rseqc_inner_distance/script.sh      |  25 ++++
 src/rseqc/rseqc_inner_distance/test.sh        |  77 ++++++++++++
 .../rseqc_inner_distance/test_data/test.bed12 |   4 +
 .../test_data/test.paired_end.sorted.bam      | Bin 0 -> 10205 bytes
 .../test_data/test1.inner_distance.txt        |  49 ++++++++
 .../test_data/test1.inner_distance_freq.txt   | 100 +++++++++++++++
 .../test_data/test2.inner_distance.txt        |   4 +
 .../test_data/test2.inner_distance_freq.txt   | 100 +++++++++++++++
 11 files changed, 519 insertions(+)
 create mode 100644 src/rseqc/rseqc_inner_distance/config.vsh.yaml
 create mode 100644 src/rseqc/rseqc_inner_distance/help.txt
 create mode 100644 src/rseqc/rseqc_inner_distance/script.sh
 create mode 100644 src/rseqc/rseqc_inner_distance/test.sh
 create mode 100644 src/rseqc/rseqc_inner_distance/test_data/test.bed12
 create mode 100644 src/rseqc/rseqc_inner_distance/test_data/test.paired_end.sorted.bam
 create mode 100644 src/rseqc/rseqc_inner_distance/test_data/test1.inner_distance.txt
 create mode 100644 src/rseqc/rseqc_inner_distance/test_data/test1.inner_distance_freq.txt
 create mode 100644 src/rseqc/rseqc_inner_distance/test_data/test2.inner_distance.txt
 create mode 100644 src/rseqc/rseqc_inner_distance/test_data/test2.inner_distance_freq.txt

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3fc134fd..0e32edb1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,7 @@
 * `rsem/rsem_calculate_expression`: Calculate expression levels (PR #93).
 
 * `rseqc`:
+  - `rseqc/rseqc_inner_distance`: Calculate inner distance between read pairs (PR #159).
   - `rseqc/rseqc_inferexperiment`: Infer strandedness from sequencing reads (PR #158).
   - `rseqc/bam_stat`: Generate statistics from a bam file (PR #155).
 
diff --git a/src/rseqc/rseqc_inner_distance/config.vsh.yaml b/src/rseqc/rseqc_inner_distance/config.vsh.yaml
new file mode 100644
index 00000000..e050bb24
--- /dev/null
+++ b/src/rseqc/rseqc_inner_distance/config.vsh.yaml
@@ -0,0 +1,116 @@
+name: "rseqc_inner_distance"
+namespace: "rseqc"
+description: |
+  Calculate inner distance between read pairs.
+links:
+  homepage: https://rseqc.sourceforge.net/
+  documentation: https://rseqc.sourceforge.net/#inner-distance-py
+  issue_tracker: https://github.com/MonashBioinformaticsPlatform/RSeQC/issues
+  repository: https://github.com/MonashBioinformaticsPlatform/RSeQC
+references:
+  doi: 10.1093/bioinformatics/bts356
+license: GPL-3.0
+authors:
+  - __merge__: /src/_authors/emma_rousseau.yaml
+    roles: [ author, maintainer ]
+
+argument_groups:
+- name: "Input"
+  arguments: 
+  - name: "--input_file"
+    alternatives: ["-i"]
+    type: file 
+    required: true
+    description: input alignment file in BAM or SAM format
+
+  - name: "--refgene"
+    alternatives: ["-r"]
+    type: file 
+    required: true
+    description: Reference gene model in bed format
+
+  - name: "--sample_size"
+    alternatives: ["-k"]
+    type: integer
+    example: 1000000
+    description: Numer of reads sampled from SAM/BAM file, default = 1000000.
+  
+  - name: "--mapq"
+    alternatives: ["-q"]
+    type: integer
+    example: 30 
+    description: Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30.
+
+  - name: "--lower_bound"
+    alternatives: ["-l"]
+    type: integer
+    example: -250 
+    description: Lower bound of inner distance (bp). This option is used for ploting histograme, default=-250.
+
+  - name: "--upper_bound"
+    alternatives: ["-u"]
+    type: integer
+    example: 250 
+    description: Upper bound of inner distance (bp). This option is used for ploting histograme, default=250.
+
+  - name: "--step"
+    alternatives: ["-s"]
+    type: integer
+    example: 5 
+    description: Step size (bp) of histograme. This option is used for plotting histogram, default=5.
+
+- name: "Output"
+  arguments: 
+  - name: "--output_prefix"
+    alternatives: ["-o"]
+    type: string
+    required: true
+    description: Rrefix of output files.
+
+  - name: "--output_stats"
+    type: file
+    direction: output
+    description: output file (txt) with summary statistics of inner distances of paired reads
+
+  - name: "--output_dist"
+    type: file
+    direction: output
+    description: output file (txt) with inner distances of all paired reads
+
+  - name: "--output_freq"
+    type: file
+    direction: output
+    description: output file (txt) with frequencies of inner distances of all paired reads
+
+  - name: "--output_plot"
+    type: file
+    direction: output
+    description: output file (pdf) with histogram plot of of inner distances of all paired reads
+
+  - name: "--output_plot_r"
+    type: file
+    direction: output
+    description: output file (R) with script of histogram plot of of inner distances of all paired reads
+    
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - path: test_data
+  
+engines:
+- type: docker
+  image: python:3.10
+  setup:   
+    - type: apt
+      packages: [r-base]
+    - type: python
+      packages: [ RSeQC ]
+    - type: docker
+      run: |
+        echo "RSeQC - inner_distance.py: $(inner_distance.py --version | cut -d' ' -f2)" > /var/software_versions.txt
+runners: 
+- type: executable
+- type: nextflow
\ No newline at end of file
diff --git a/src/rseqc/rseqc_inner_distance/help.txt b/src/rseqc/rseqc_inner_distance/help.txt
new file mode 100644
index 00000000..18f97bb6
--- /dev/null
+++ b/src/rseqc/rseqc_inner_distance/help.txt
@@ -0,0 +1,43 @@
+```
+inner_distance.py --help
+```
+
+Usage: inner_distance.py [options]
+
+Calculate the inner distance (insert size)  of RNA-seq fragments. 
+
+               RNA fragment
+ _________________||_________________
+|                                    |
+|                                    |
+||||||||||------------------||||||||||
+  read_1      insert_size     read_2
+
+fragment size = read_1 + insert_size + read_2
+
+
+
+Options:
+  --version             show program's version number and exit
+  -h, --help            show this help message and exit
+  -i INPUT_FILE, --input-file=INPUT_FILE
+                        Alignment file in BAM or SAM format.
+  -o OUTPUT_PREFIX, --out-prefix=OUTPUT_PREFIX
+                        Prefix of output files(s)
+  -r REF_GENE, --refgene=REF_GENE
+                        Reference gene model in BED format.
+  -k SAMPLESIZE, --sample-size=SAMPLESIZE
+                        Number of read-pairs used to estimate inner distance.
+                        default=1000000
+  -l LOWER_BOUND_SIZE, --lower-bound=LOWER_BOUND_SIZE
+                        Lower bound of inner distance (bp). This option is
+                        used for ploting histograme. default=-250
+  -u UPPER_BOUND_SIZE, --upper-bound=UPPER_BOUND_SIZE
+                        Upper bound of inner distance (bp). This option is
+                        used for plotting histogram. default=250
+  -s STEP_SIZE, --step=STEP_SIZE
+                        Step size (bp) of histograme. This option is used for
+                        plotting histogram. default=5
+  -q MAP_QUAL, --mapq=MAP_QUAL
+                        Minimum mapping quality (phred scaled) for an
+                        alignment to be called "uniquely mapped". default=30
\ No newline at end of file
diff --git a/src/rseqc/rseqc_inner_distance/script.sh b/src/rseqc/rseqc_inner_distance/script.sh
new file mode 100644
index 00000000..fe00c590
--- /dev/null
+++ b/src/rseqc/rseqc_inner_distance/script.sh
@@ -0,0 +1,25 @@
+#!/bin/bash
+
+set -exo pipefail 
+
+
+inner_distance.py \
+    -i $par_input_file \
+    -r $par_refgene \
+    -o $par_output_prefix \
+    ${par_sample_size:+-k "${par_sample_size}"} \
+    ${par_lower_bound:+-l "${par_lower_bound}"} \
+    ${par_upper_bound:+-u "${par_upper_bound}"} \
+    ${par_step:+-s "${par_step}"} \
+    ${par_mapq:+-q "${par_mapq}"} \
+> stdout.txt
+
+if [[ -n $par_output_stats ]]; then head -n 2 stdout.txt > $par_output_stats; fi
+
+
+[[ -n "$par_output_dist" && -f "$par_output_prefix.inner_distance.txt" ]] && mv $par_output_prefix.inner_distance.txt $par_output_dist
+[[ -n "$par_output_plot" && -f "$par_output_prefix.inner_distance_plot.pdf" ]] && mv $par_output_prefix.inner_distance_plot.pdf $par_output_plot
+[[ -n "$par_output_plot_r" && -f "$par_output_prefix.inner_distance_plot.r" ]] && mv $par_output_prefix.inner_distance_plot.r $par_output_plot_r
+[[ -n "$par_output_freq" && -f "$par_output_prefix.inner_distance_freq.txt" ]] && mv $par_output_prefix.inner_distance_freq.txt $par_output_freq
+
+exit 0
\ No newline at end of file
diff --git a/src/rseqc/rseqc_inner_distance/test.sh b/src/rseqc/rseqc_inner_distance/test.sh
new file mode 100644
index 00000000..927a69a9
--- /dev/null
+++ b/src/rseqc/rseqc_inner_distance/test.sh
@@ -0,0 +1,77 @@
+#!/bin/bash
+
+
+# define input and output for script
+input_bam="$meta_resources_dir/test_data/test.paired_end.sorted.bam"
+input_bed="$meta_resources_dir/test_data/test.bed12"
+
+output_stats="inner_distance_stats.txt"
+output_dist="inner_distance.txt"
+output_plot="inner_distance_plot.pdf"
+output_plot_r="inner_distance_plot.r"
+output_freq="inner_distance_freq.txt"
+
+# Run executable
+echo "> Running $meta_functionality_name"
+
+"$meta_executable" \
+    --input_file $input_bam \
+    --refgene $input_bed \
+    --output_prefix "test" \
+    --output_stats $output_stats \
+    --output_dist $output_dist \
+    --output_plot $output_plot \
+    --output_plot_r $output_plot_r \
+    --output_freq $output_freq
+
+exit_code=$?
+[[ $exit_code != 0 ]] && echo "Non zero exit code: $exit_code" && exit 1
+
+echo ">> Check whether output is present and not empty"
+
+[[ -f "$output_stats" ]] || { echo "$output_stats was not created"; exit 1; }
+[[ -s "$output_stats" ]] || { echo "$output_stats is empty"; exit 1; }
+[[ -f "$output_dist" ]] || { echo "$output_dist was not created"; exit 1; }
+[[ -s "$output_dist" ]] || { echo "$output_dist is empty"; exit 1; }
+[[ -f "$output_plot" ]] || { echo "$output_plot was not created"; exit 1; }
+[[ -s "$output_plot" ]] || { echo "$output_plot is empty"; exit 1; }
+[[ -f "$output_plot_r" ]] || { echo "$output_plot_r was not created"; exit 1; }
+[[ -s "$output_plot_r" ]] || { echo "$output_plot_r is empty"; exit 1; }
+[[ -f "$output_freq" ]] || { echo "$output_freq was created"; exit 1; }
+[[ -s "$output_freq" ]] || { echo "$output_freq is empty"; exit 1; }
+
+echo ">> Check whether output is correct"
+diff "$output_freq" "$meta_resources_dir/test_data/test1.inner_distance_freq.txt" || { echo "Output is not correct"; exit 1; }
+diff "$output_dist" "$meta_resources_dir/test_data/test1.inner_distance.txt" || { echo "Output is not correct"; exit 1; }
+
+# clean up
+rm "$output_stats" "$output_dist" "$output_plot" "$output_plot_r" "$output_freq"
+################################################################################
+
+echo "> Running $meta_functionality_name with non-default parameters and default output file names"
+"$meta_executable" \
+    --input_file $input_bam \
+    --refgene $input_bed \
+    --output_prefix "test" \
+    --sample_size 4 \
+    --mapq 10
+
+exit_code=$?
+[[ $exit_code != 0 ]] && echo "Non zero exit code: $exit_code" && exit 1
+
+echo ">> Check whether output is present and not empty"
+
+[[ -f "test.inner_distance.txt" ]] || { echo "test.inner_distance.txt was not created"; exit 1; }
+[[ -s "test.inner_distance.txt" ]] || { echo "test.inner_distance.txt is empty"; exit 1; }
+[[ -f "test.inner_distance_plot.pdf" ]] || { echo "test.inner_distance_plot.pdf was not created"; exit 1; }
+[[ -s "test.inner_distance_plot.pdf" ]] || { echo "test.inner_distance_plot.pdf is empty"; exit 1; }
+[[ -f "test.inner_distance_plot.r" ]] || { echo "test.inner_distance_plot.r was not created"; exit 1; }
+[[ -s "test.inner_distance_plot.r" ]] || { echo "test.inner_distance_plot.r is empty"; exit 1; }
+[[ -f "test.inner_distance_freq.txt" ]] || { echo "test.inner_distance_freq.txt was created"; exit 1; }
+[[ -s "test.inner_distance_freq.txt" ]] || { echo "test.inner_distance_freq.txt is empty"; exit 1; }
+
+echo ">> Check whether output is correct"
+diff "test.inner_distance_freq.txt" "$meta_resources_dir/test_data/test2.inner_distance_freq.txt" || { echo "Output is not correct"; exit 1; }
+diff "test.inner_distance.txt" "$meta_resources_dir/test_data/test2.inner_distance.txt" || { echo "Output is not correct"; exit 1; }
+
+exit 0
\ No newline at end of file
diff --git a/src/rseqc/rseqc_inner_distance/test_data/test.bed12 b/src/rseqc/rseqc_inner_distance/test_data/test.bed12
new file mode 100644
index 00000000..33a46951
--- /dev/null
+++ b/src/rseqc/rseqc_inner_distance/test_data/test.bed12
@@ -0,0 +1,4 @@
+MT192765.1	1242	1264	nCoV-2019_5_LEFT	1	+	1242	1264	0	2	10,12,	0,10,
+MT192765.1	1573	1595	nCoV-2019_6_LEFT	2	+	1573	1595	0	2	7,15,	0,7,
+MT192765.1	1623	1651	nCoV-2019_5_RIGHT	1	-	1623	1651	0	2	14,14,	0,14,
+MT192765.1	1942	1964	nCoV-2019_6_RIGHT	2	-	1942	1964	0	2	11,11	0,11,
diff --git a/src/rseqc/rseqc_inner_distance/test_data/test.paired_end.sorted.bam b/src/rseqc/rseqc_inner_distance/test_data/test.paired_end.sorted.bam
new file mode 100644
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diff --git a/src/rseqc/rseqc_inner_distance/test_data/test1.inner_distance.txt b/src/rseqc/rseqc_inner_distance/test_data/test1.inner_distance.txt
new file mode 100644
index 00000000..e5f09f8f
--- /dev/null
+++ b/src/rseqc/rseqc_inner_distance/test_data/test1.inner_distance.txt
@@ -0,0 +1,49 @@
+ERR5069949.29668	-4	sameTranscript=No,dist=genomic
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diff --git a/src/rseqc/rseqc_inner_distance/test_data/test1.inner_distance_freq.txt b/src/rseqc/rseqc_inner_distance/test_data/test1.inner_distance_freq.txt
new file mode 100644
index 00000000..908326ff
--- /dev/null
+++ b/src/rseqc/rseqc_inner_distance/test_data/test1.inner_distance_freq.txt
@@ -0,0 +1,100 @@
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diff --git a/src/rseqc/rseqc_inner_distance/test_data/test2.inner_distance.txt b/src/rseqc/rseqc_inner_distance/test_data/test2.inner_distance.txt
new file mode 100644
index 00000000..a1930c9e
--- /dev/null
+++ b/src/rseqc/rseqc_inner_distance/test_data/test2.inner_distance.txt
@@ -0,0 +1,4 @@
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diff --git a/src/rseqc/rseqc_inner_distance/test_data/test2.inner_distance_freq.txt b/src/rseqc/rseqc_inner_distance/test_data/test2.inner_distance_freq.txt
new file mode 100644
index 00000000..021311a2
--- /dev/null
+++ b/src/rseqc/rseqc_inner_distance/test_data/test2.inner_distance_freq.txt
@@ -0,0 +1,100 @@
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