From 2f8bf020dd5f391bbb3260ad33fa73b6094cae19 Mon Sep 17 00:00:00 2001
From: Emma Rousseau <emmarou1@icloud.com>
Date: Sat, 26 Oct 2024 20:39:23 +0200
Subject: [PATCH] Rseq bamstat (#155)

* initial commit dedup

* Revert "initial commit dedup"

This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.

* initial commit

* add test, test data, version, help

* Update CHANGELOG.md

* adjust argument names, reduce test data size

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
Co-authored-by: Kai Waldrant <kai@data-intuitive.com>
---
 CHANGELOG.md                                  |   9 +--
 src/rseqc/rseqc_bamstat/config.vsh.yaml       |  59 ++++++++++++++++++
 src/rseqc/rseqc_bamstat/help.txt              |  18 ++++++
 src/rseqc/rseqc_bamstat/script.sh             |   9 +++
 src/rseqc/rseqc_bamstat/test.sh               |  49 +++++++++++++++
 .../rseqc_bamstat/test_data/ref_output.txt    |  22 +++++++
 .../test_data/ref_output_mapq.txt             |  22 +++++++
 src/rseqc/rseqc_bamstat/test_data/sample.bam  | Bin 0 -> 9240 bytes
 8 files changed, 184 insertions(+), 4 deletions(-)
 create mode 100644 src/rseqc/rseqc_bamstat/config.vsh.yaml
 create mode 100644 src/rseqc/rseqc_bamstat/help.txt
 create mode 100644 src/rseqc/rseqc_bamstat/script.sh
 create mode 100644 src/rseqc/rseqc_bamstat/test.sh
 create mode 100644 src/rseqc/rseqc_bamstat/test_data/ref_output.txt
 create mode 100644 src/rseqc/rseqc_bamstat/test_data/ref_output_mapq.txt
 create mode 100644 src/rseqc/rseqc_bamstat/test_data/sample.bam

diff --git a/CHANGELOG.md b/CHANGELOG.md
index dcc783c9..5f720035 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,16 +16,17 @@
 
 * `rsem/rsem_calculate_expression`: Calculate expression levels (PR #93).
 
-* `nanoplot`: Plotting tool for long read sequencing data and alignments (PR #95).
+* `rseqc`:
+  - `rseqc/bam_stat`: Generate statistics from a bam file (PR #155).
 
+* `nanoplot`: Plotting tool for long read sequencing data and alignments (PR #95).
 
-## BREAKING CHANGES
+## BUG FIXES
 
 * `falco`: Fix a typo in the `--reverse_complement` argument (PR #157).
 
-## BUG FIXES
+* `cutadapt`: Fix the the non-functional `action` parameter (PR #161).
 
-* `cutadapt`: fix the the non-functional `action` parameter (PR #161).
 
 ## MINOR CHANGES
 
diff --git a/src/rseqc/rseqc_bamstat/config.vsh.yaml b/src/rseqc/rseqc_bamstat/config.vsh.yaml
new file mode 100644
index 00000000..6d607e2f
--- /dev/null
+++ b/src/rseqc/rseqc_bamstat/config.vsh.yaml
@@ -0,0 +1,59 @@
+name: rseqc_bamstat
+namespace: rseqc
+keywords: [ rnaseq, genomics ]
+description: Generate statistics from a bam file.
+links:
+  homepage: https://rseqc.sourceforge.net/
+  documentation: https://rseqc.sourceforge.net/#bam-stat-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: "--mapq"
+    alternatives: -q
+    type: integer
+    example: 30 
+    description: |
+      Minimum mapping quality (phred scaled) to determine uniquely mapped reads. Default: '30'.
+    
+- name: "Output"
+  arguments: 
+  - name: "--output"
+    type: file
+    direction: output
+    description: Output file (txt) with mapping quality statistics.
+
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+  
+engines:
+- type: docker
+  image: python:3.10
+  setup:
+    - type: python
+      packages: [ RSeQC ]
+    - type: docker
+      run: |
+        echo "RSeQC bam_stat.py: $(bam_stat.py --version | cut -d' ' -f2-)" > /var/software_versions.txt
+runners: 
+- type: executable
+- type: nextflow
diff --git a/src/rseqc/rseqc_bamstat/help.txt b/src/rseqc/rseqc_bamstat/help.txt
new file mode 100644
index 00000000..b4e9c1d9
--- /dev/null
+++ b/src/rseqc/rseqc_bamstat/help.txt
@@ -0,0 +1,18 @@
+```
+bam_stat.py -h
+```
+
+Usage: bam_stat.py [options]
+
+Summarizing mapping statistics of a BAM or SAM file. 
+
+
+
+Options:
+  --version             show program's version number and exit
+  -h, --help            show this help message and exit
+  -i INPUT_FILE, --input-file=INPUT_FILE
+                        Alignment file in BAM or SAM format.
+  -q MAP_QUAL, --mapq=MAP_QUAL
+                        Minimum mapping quality (phred scaled) to determine
+                        "uniquely mapped" reads. default=30
\ No newline at end of file
diff --git a/src/rseqc/rseqc_bamstat/script.sh b/src/rseqc/rseqc_bamstat/script.sh
new file mode 100644
index 00000000..32927bb6
--- /dev/null
+++ b/src/rseqc/rseqc_bamstat/script.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+
+set -eo pipefail 
+
+bam_stat.py \
+    --input-file "${par_input_file}" \
+    ${par_mapq:+--mapq "${par_mapq}"} \
+> $par_output
diff --git a/src/rseqc/rseqc_bamstat/test.sh b/src/rseqc/rseqc_bamstat/test.sh
new file mode 100644
index 00000000..f9180da8
--- /dev/null
+++ b/src/rseqc/rseqc_bamstat/test.sh
@@ -0,0 +1,49 @@
+#!/bin/bash
+
+# define input and output for script
+
+input_bam="sample.bam"
+output_summary="mapping_quality.txt"
+
+# run executable and tests
+echo "> Running $meta_functionality_name."
+
+"$meta_executable" \
+    --input_file "$meta_resources_dir/test_data/$input_bam" \
+    --output "$output_summary"
+
+exit_code=$?
+[[ $exit_code != 0 ]] && echo "Non zero exit code: $exit_code" && exit 1
+
+echo ">> Checking whether output is present"
+[ ! -f "$output_summary" ] && echo "$output_summary file missing" && exit 1
+[ ! -s "$output_summary" ] && echo "$output_summary file is empty" && exit 1
+
+echo ">> Checking whether output is correct"
+diff "$meta_resources_dir/test_data/ref_output.txt" "$meta_resources_dir/$output_summary" || { echo "Output is not correct"; exit 1; }
+
+#############################################################################
+
+echo ">>> Test 2: Test with non-default mapping quality threshold"
+
+output_summary="mapping_quality_mapq_50.txt"
+
+# run executable and tests
+echo "> Running $meta_functionality_name."
+
+"$meta_executable" \
+    --input_file "$meta_resources_dir/test_data/$input_bam" \
+    --output "$output_summary" \
+    --mapq 50
+
+exit_code=$?
+[[ $exit_code != 0 ]] && echo "Non zero exit code: $exit_code" && exit 1
+
+echo ">> Checking whether output is present"
+[ ! -f "$output_summary" ] && echo "$output_summary file missing" && exit 1
+[ ! -s "$output_summary" ] && echo "$output_summary file is empty" && exit 1
+
+echo ">> Checking whether output is correct"
+diff "$meta_resources_dir/test_data/ref_output_mapq.txt" "$meta_resources_dir/$output_summary" || { echo "Output is not correct"; exit 1; }
+
+exit 0
\ No newline at end of file
diff --git a/src/rseqc/rseqc_bamstat/test_data/ref_output.txt b/src/rseqc/rseqc_bamstat/test_data/ref_output.txt
new file mode 100644
index 00000000..6b939096
--- /dev/null
+++ b/src/rseqc/rseqc_bamstat/test_data/ref_output.txt
@@ -0,0 +1,22 @@
+
+#==================================================
+#All numbers are READ count
+#==================================================
+
+Total records:                          90
+
+QC failed:                              0
+Optical/PCR duplicate:                  0
+Non primary hits                        0
+Unmapped reads:                         1
+mapq < mapq_cut (non-unique):           0
+
+mapq >= mapq_cut (unique):              89
+Read-1:                                 45
+Read-2:                                 44
+Reads map to '+':                       44
+Reads map to '-':                       45
+Non-splice reads:                       89
+Splice reads:                           0
+Reads mapped in proper pairs:           88
+Proper-paired reads map to different chrom:0
diff --git a/src/rseqc/rseqc_bamstat/test_data/ref_output_mapq.txt b/src/rseqc/rseqc_bamstat/test_data/ref_output_mapq.txt
new file mode 100644
index 00000000..be8af62f
--- /dev/null
+++ b/src/rseqc/rseqc_bamstat/test_data/ref_output_mapq.txt
@@ -0,0 +1,22 @@
+
+#==================================================
+#All numbers are READ count
+#==================================================
+
+Total records:                          90
+
+QC failed:                              0
+Optical/PCR duplicate:                  0
+Non primary hits                        0
+Unmapped reads:                         1
+mapq < mapq_cut (non-unique):           6
+
+mapq >= mapq_cut (unique):              83
+Read-1:                                 42
+Read-2:                                 41
+Reads map to '+':                       44
+Reads map to '-':                       39
+Non-splice reads:                       83
+Splice reads:                           0
+Reads mapped in proper pairs:           83
+Proper-paired reads map to different chrom:0
diff --git a/src/rseqc/rseqc_bamstat/test_data/sample.bam b/src/rseqc/rseqc_bamstat/test_data/sample.bam
new file mode 100644
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