Bedtools_bamtofastq (#101)

* Initial Commit

* update

* update

* Config file and Script.sh

* Test Script

* adding test

* working on testing

* Fixing Bugs

* Working version

* Update CHANGELOG.md

* Required Changes

* Adding exit on error

* adding more links

CHANGELOG.md

@@ -30,6 +30,11 @@
 
 * `agat/agat_convert_embl2gff`: convert an EMBL file into GFF format (PR #99).
 
+* `bedtools`:
+    - `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94).
+    - `bedtools/bedtools_sort`: Sorts a feature file (bed/gff/vcf) by chromosome and other criteria (PR #98).
+    - `bedtools/bedtools_bamtofastq`: Convert BAM alignments to FASTQ files (PR #101).
+
 ## MINOR CHANGES
 
 * `busco` components: update BUSCO to `5.7.1` (PR #72).

src/bedtools/bedtools_bamtofastq/config.vsh.yaml

@@ -0,0 +1,74 @@
+name: bedtools_bamtofastq
+namespace: bedtools
+description: | 
+  Conversion tool for extracting FASTQ records from sequence alignments in BAM format.
+keywords: [Conversion ,BAM, FASTQ]
+links:
+  documentation: https://bedtools.readthedocs.io/en/latest/content/tools/bamtofastq.html
+  repository: https://github.com/arq5x/bedtools2
+  homepage: https://bedtools.readthedocs.io/en/latest/#
+  issue_tracker: https://github.com/arq5x/bedtools2/issues
+references:
+  doi: 10.1093/bioinformatics/btq033
+license: MIT
+requirements:
+  commands: [bedtools]
+authors:
+  - __merge__: /src/_authors/theodoro_gasperin.yaml
+    roles: [ author, maintainer ]
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --input
+        alternatives: -i
+        type: file
+        description: Input BAM file to be converted to FASTQ.
+        required: true
+
+  - name: Outputs
+    arguments:
+      - name: --fastq
+        alternatives: -fq
+        direction: output
+        type: file
+        description: Output FASTQ file.
+        required: true
+
+      - name: --fastq2
+        alternatives: -fq2
+        type: file
+        direction: output
+        description: |
+          FASTQ for second end. Used if BAM contains paired-end data.
+          BAM should be sorted by query name is creating paired FASTQ.
+         
+  - name: Options
+    arguments:
+      - name: --tags
+        type: boolean_true
+        description: |
+          Create FASTQ based on the mate info in the BAM R2 and Q2 tags.
+
+resources:
+  - type: bash_script
+    path: script.sh
+
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - path: test_data
+
+engines:
+  - type: docker
+    image: debian:stable-slim
+    setup:
+      - type: apt
+        packages: [bedtools, procps]
+      - type: docker
+        run: |
+          echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var/software_versions.txt
+
+runners:
+  - type: executable
+  - type: nextflow

src/bedtools/bedtools_bamtofastq/help.txt

@@ -0,0 +1,25 @@
+```bash
+bedtools bamtofastq
+```
+
+Tool:    bedtools bamtofastq (aka bamToFastq)
+Version: v2.30.0
+Summary: Convert BAM alignments to FASTQ files. 
+
+Usage:   bamToFastq [OPTIONS] -i <BAM> -fq <FQ> 
+
+Options:
+	-fq2	FASTQ for second end.  Used if BAM contains paired-end data.
+		BAM should be sorted by query name is creating paired FASTQ.
+
+	-tags	Create FASTQ based on the mate info
+		in the BAM R2 and Q2 tags.
+
+Tips: 
+	If you want to create a single, interleaved FASTQ file 
+	for paired-end data, you can just write both to /dev/stdout:
+
+	bedtools bamtofastq -i x.bam -fq /dev/stdout -fq2 /dev/stdout > x.ilv.fq
+
+	Also, the samtools fastq command has more fucntionality and is a useful alternative.
+

src/bedtools/bedtools_bamtofastq/script.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# Exit on error
+set -eo pipefail
+
+# Unset parameters
+[[ "$par_tags" == "false" ]] && unset par_tags
+
+# Execute bedtools bamtofastq with the provided arguments
+bedtools bamtofastq \
+    ${par_tags:+-tags} \
+    ${par_fastq2:+-fq2 "$par_fastq2"} \
+    -i "$par_input" \
+    -fq "$par_fastq"
+
+

src/bedtools/bedtools_bamtofastq/test.sh

@@ -0,0 +1,84 @@
+#!/bin/bash
+
+# exit on error
+set -eo pipefail
+
+test_data="$meta_resources_dir/test_data"
+
+#############################################
+# helper functions
+assert_file_exists() {
+  [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
+}
+assert_file_not_empty() {
+  [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
+}
+assert_file_contains() {
+  grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
+}
+assert_identical_content() {
+  diff -a "$2" "$1" \
+    || (echo "Files are not identical!" && exit 1)
+}
+#############################################
+
+# Test 1: normal conversion 
+mkdir test1
+cd test1
+
+echo "> Run bedtools bamtofastq on BAM file"
+"$meta_executable" \
+  --input "$test_data/example.bam" \
+  --fastq "output.fastq"
+
+# checks
+assert_file_exists "output.fastq"
+assert_file_not_empty "output.fastq"
+assert_identical_content "output.fastq" "$test_data/expected.fastq"
+echo "- test1 succeeded -"
+
+cd ..
+
+# Test 2: with tags
+mkdir test2
+cd test2
+
+echo "> Run bedtools bamtofastq on BAM file with tags"
+"$meta_executable" \
+  --input "$test_data/example.bam" \
+  --fastq "output.fastq" \
+  --tags
+
+# checks
+assert_file_exists "output.fastq"
+assert_file_not_empty "output.fastq"
+assert_identical_content "output.fastq" "$test_data/expected.fastq"
+echo "- test2 succeeded -"
+
+cd ..
+
+# Test 3: with option fq2
+mkdir test3
+cd test3
+
+echo "> Run bedtools bamtofastq on BAM file with output_fq2"
+"$meta_executable" \
+  --input "$test_data/example.bam" \
+  --fastq "output1.fastq" \
+  --fastq2 "output2.fastq" 
+
+# checks
+assert_file_exists "output1.fastq"
+assert_file_not_empty "output1.fastq"
+assert_identical_content "output1.fastq" "$test_data/expected_1.fastq"
+assert_file_exists "output2.fastq"
+assert_file_not_empty "output2.fastq"
+assert_identical_content "output2.fastq" "$test_data/expected_2.fastq"
+echo "- test3 succeeded -"
+
+cd ..
+
+echo "All tests succeeded"
+exit 0
+
+

src/bedtools/bedtools_bamtofastq/test_data/example.sam

@@ -0,0 +1,3 @@
+@SQ	SN:chr2:172936693-172938111	LN:1418
+my_read	99	chr2:172936693-172938111	129	60	100M	=	429	400	CTAACTAGCCTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCTACTGGGAAAAGAAATTTAATGCATATCTCACT	*	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:100
+my_read	147	chr2:172936693-172938111	429	60	100M	=	129	-400	TCGAGCTCTGCATTCATGGCTGTGTCTAAAGGGCATGTCAGCCTTTGATTCTCTCTGAGAGGTAATTATCCTTTTCCTGTCACGGAACAACAAATGATAG	*	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:100

src/bedtools/bedtools_bamtofastq/test_data/expected.fastq

@@ -0,0 +1,16 @@
+@my_read
+CTAACTAGCCTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCTACTGGGAAAAGAAATTTAATGCATATCTCACT
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+@my_read
+CTAACTAGCCTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCTACTGGGAAAAGAAATTTAATGCATATCTCACT
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+@my_read
+CTATCATTTGTTGTTCCGTGACAGGAAAAGGATAATTACCTCTCAGAGAGAATCAAAGGCTGACATGCCCTTTAGACACAGCCATGAATGCAGAGCTCGA
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+@my_read
+CTATCATTTGTTGTTCCGTGACAGGAAAAGGATAATTACCTCTCAGAGAGAATCAAAGGCTGACATGCCCTTTAGACACAGCCATGAATGCAGAGCTCGA
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

src/bedtools/bedtools_bamtofastq/test_data/expected_1.fastq

@@ -0,0 +1,4 @@
+@my_read/1
+CTAACTAGCCTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCTACTGGGAAAAGAAATTTAATGCATATCTCACT
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

src/bedtools/bedtools_bamtofastq/test_data/expected_2.fastq

@@ -0,0 +1,4 @@
+@my_read/2
+CTATCATTTGTTGTTCCGTGACAGGAAAAGGATAATTACCTCTCAGAGAGAATCAAAGGCTGACATGCCCTTTAGACACAGCCATGAATGCAGAGCTCGA
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

src/bedtools/bedtools_bamtofastq/test_data/script.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+# create sam file
+printf "@SQ\tSN:chr2:172936693-172938111\tLN:1418\n" > example.sam
+printf "my_read\t99\tchr2:172936693-172938111\t129\t60\t100M\t=\t429\t400\tCTAACTAGCCTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCTACTGGGAAAAGAAATTTAATGCATATCTCACT\t*\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:100\n" >> example.sam
+printf "my_read\t147\tchr2:172936693-172938111\t429\t60\t100M\t=\t129\t-400\tTCGAGCTCTGCATTCATGGCTGTGTCTAAAGGGCATGTCAGCCTTTGATTCTCTCTGAGAGGTAATTATCCTTTTCCTGTCACGGAACAACAAATGATAG\t*\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:100\n" >> example.sam
+
+# create bam file
+# samtools view -b example.sam > example.bam
+
+# create fastq files
+# bedtools bamtofastq -i example.bam -fq expected.fastq
+# bedtools bamtofastq -i example.bam -fq expected_1.fastq -fq2 expected_2.fastq