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- still need to add content check using samtools view
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,143 @@ | ||
| #!/bin/bash | ||
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| # exit on error | ||
| set -eo pipefail | ||
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| ############################################# | ||
| # 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" "$1" \ | ||
| || (echo "Files are not identical!" && exit 1) | ||
| } | ||
| ############################################# | ||
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| # Create directories for tests | ||
| echo "Creating Test Data..." | ||
| mkdir -p test_data | ||
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| # Create and populate input files | ||
| printf "chr1\t248956422\nchr3\t242193529\nchr2\t198295559\n" > "test_data/genome.txt" | ||
| printf "chr2:172936693-172938111\t128\t228\tmy_read/1\t37\t+\nchr2:172936693-172938111\t428\t528\tmy_read/2\t37\t-\n" > "test_data/example.bed" | ||
| printf "chr2:172936693-172938111\t128\t228\tmy_read/1\t60\t+\t128\t228\t255,0,0\t1\t100\t0\nchr2:172936693-172938111\t428\t528\tmy_read/2\t60\t-\t428\t528\t255,0,0\t1\t100\t0\n" > "test_data/example.bed12" | ||
| # Create and populate example.gff file | ||
| printf "##gff-version 3\n" > "test_data/example.gff" | ||
| printf "chr1\t.\tgene\t1000\t2000\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/example.gff" | ||
| printf "chr3\t.\tmRNA\t1000\t2000\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/example.gff" | ||
| printf "chr1\t.\texon\t1000\t1200\t.\t+\t.\tID=exon1;Parent=transcript1\n" >> "test_data/example.gff" | ||
| printf "chr2\t.\texon\t1500\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/example.gff" | ||
| printf "chr1\t.\tCDS\t1000\t1200\t.\t+\t0\tID=cds1;Parent=transcript1\n" >> "test_data/example.gff" | ||
| printf "chr1\t.\tCDS\t1500\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/example.gff" | ||
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| # Test 1: Default conversion BED to BAM | ||
| mkdir test1 | ||
| cd test1 | ||
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| echo "> Run bedtools_bedtobam on BED file" | ||
| "$meta_executable" \ | ||
| --input "../test_data/example.bed" \ | ||
| --genome "../test_data/genome.txt" \ | ||
| --output "output.bam" | ||
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| # checks | ||
| assert_file_exists "output.bam" | ||
| assert_file_not_empty "output.bam" | ||
| echo "- test1 succeeded -" | ||
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| cd .. | ||
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| # I could not assert_identical_content (bam file is compressed and -ubam option does not seem to work on this version). | ||
| # could use samtools view to check the content of the bam file, would need to add samtools as a dependency. | ||
| # TODO: check if older versions works with -ubam option!!! | ||
| # Version 2.27.1 (bedtools) -ubam outputs better than version 2.30.0 (bedtools). | ||
| # However, its output is still somewhat compressed. | ||
|
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| # Test 2: BED12 file | ||
| mkdir test2 | ||
| cd test2 | ||
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| echo "> Run bedtools_bedtobam on BED12 file" | ||
| "$meta_executable" \ | ||
| --input "../test_data/example.bed12" \ | ||
| --genome "../test_data/genome.txt" \ | ||
| --output "output.bam" \ | ||
| --bed12 \ | ||
| # --uncompress_bam | ||
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| # checks | ||
| assert_file_exists "output.bam" | ||
| assert_file_not_empty "output.bam" | ||
| # assert_identical_content "output.bam" "../test_data/expected12.sam" | ||
| echo "- test2 succeeded -" | ||
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| cd .. | ||
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| # Test 3: Uncompressed BAM file | ||
| mkdir test3 | ||
| cd test3 | ||
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| echo "> Run bedtools_bedtobam on BED file with uncompressed BAM output" | ||
| "$meta_executable" \ | ||
| --input "../test_data/example.bed" \ | ||
| --genome "../test_data/genome.txt" \ | ||
| --output "output.bam" \ | ||
| --uncompress_bam | ||
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| # checks | ||
| assert_file_exists "output.bam" | ||
| assert_file_not_empty "output.bam" | ||
| # assert_identical_content "output.bam" "../test_data/expected.sam" | ||
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| echo "- test3 succeeded -" | ||
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| cd .. | ||
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| # Test 4: Map quality | ||
| mkdir test4 | ||
| cd test4 | ||
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| echo "> Run bedtools_bedtobam on BED file with map quality" | ||
| "$meta_executable" \ | ||
| --input "../test_data/example.bed" \ | ||
| --genome "../test_data/genome.txt" \ | ||
| --output "output.bam" \ | ||
| --map_quality 10 \ | ||
| # --uncompress_bam | ||
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| # checks | ||
| assert_file_exists "output.bam" | ||
| assert_file_not_empty "output.bam" | ||
| #assert_identical_content "output.bam" "../test_data/expected_mapquality.sam" | ||
| echo "- test4 succeeded -" | ||
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| cd .. | ||
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| # Test 5: gff to bam conversion | ||
| mkdir test5 | ||
| cd test5 | ||
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| echo "> Run bedtools_bedtobam on GFF file" | ||
| "$meta_executable" \ | ||
| --input "../test_data/example.gff" \ | ||
| --genome "../test_data/genome.txt" \ | ||
| --output "output.bam" | ||
| # --uncompress_bam | ||
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| # checks | ||
| assert_file_exists "output.bam" | ||
| assert_file_not_empty "output.bam" | ||
| # assert_identical_content "output.bam" "../test_data/expected_gff.sam" | ||
| echo "- test5 succeeded -" | ||
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| cd .. | ||
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| echo "---- All tests succeeded! ----" | ||
| exit 0 |