TMPDIR

viash-hub · Aug 13, 2024 · 516e018 · 516e018
1 parent 77446e2
commit 516e018
Showing 1 changed file with 72 additions and 80 deletions.
diff --git a/src/bedtools/bedtools_genomecov/test.sh b/src/bedtools/bedtools_genomecov/test.sh
@@ -30,107 +30,109 @@ assert_identical_content() {
 
 # Create directories for tests
 echo "Creating Test Data..."
-mkdir -p test_data
+TMPDIR=$(mktemp -d "$meta_temp_dir/XXXXXX")
+function clean_up {
+  [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
+}
+trap clean_up EXIT
 
 # Create and populate input files
-printf "chr1\t248956422\nchr2\t198295559\nchr3\t242193529\n" > "test_data/genome.txt"
-printf "chr2\t128\t228\tmy_read/1\t37\t+\nchr2\t428\t528\tmy_read/2\t37\t-\n" > "test_data/example.bed"
-printf "chr2\t128\t228\tmy_read/1\t60\t+\t128\t228\t255,0,0\t1\t100\t0\nchr2\t428\t528\tmy_read/2\t60\t-\t428\t528\t255,0,0\t1\t100\t0\n" > "test_data/example.bed12"
-printf "chr2\t100\t103\n" > "test_data/example_dz.bed"
+printf "chr1\t248956422\nchr2\t198295559\nchr3\t242193529\n" > "$TMPDIR/genome.txt"
+printf "chr2\t128\t228\tmy_read/1\t37\t+\nchr2\t428\t528\tmy_read/2\t37\t-\n" > "$TMPDIR/example.bed"
+printf "chr2\t128\t228\tmy_read/1\t60\t+\t128\t228\t255,0,0\t1\t100\t0\nchr2\t428\t528\tmy_read/2\t60\t-\t428\t528\t255,0,0\t1\t100\t0\n" > "$TMPDIR/example.bed12"
+printf "chr2\t100\t103\n" > "$TMPDIR/example_dz.bed"
 
 # expected outputs
-cat > "test_data/expected_default.bed" <<EOF
+cat > "$TMPDIR/expected_default.bed" <<EOF
 chr2	0	198295359	198295559	0.999999
 chr2	1	200	198295559	1.0086e-06
 chr1	0	248956422	248956422	1
 chr3	0	242193529	242193529	1
 genome	0	689445310	689445510	1
 genome	1	200	689445510	2.90088e-07
 EOF
-cat > "test_data/expected_ibam.bed" <<EOF
+cat > "$TMPDIR/expected_ibam.bed" <<EOF
 chr2:172936693-172938111	0	1218	1418	0.858956
 chr2:172936693-172938111	1	200	1418	0.141044
 genome	0	1218	1418	0.858956
 genome	1	200	1418	0.141044
 EOF
-cat > "test_data/expected_ibam_pc.bed" <<EOF
+cat > "$TMPDIR/expected_ibam_pc.bed" <<EOF
 chr2:172936693-172938111	0	1018	1418	0.717913
 chr2:172936693-172938111	1	400	1418	0.282087
 genome	0	1018	1418	0.717913
 genome	1	400	1418	0.282087
 EOF
-cat > "test_data/expected_ibam_fs.bed" <<EOF
+cat > "$TMPDIR/expected_ibam_fs.bed" <<EOF
 chr2:172936693-172938111	0	1218	1418	0.858956
 chr2:172936693-172938111	1	200	1418	0.141044
 genome	0	1218	1418	0.858956
 genome	1	200	1418	0.141044
 EOF
-cat > "test_data/expected_dz.bed" <<EOF
+cat > "$TMPDIR/expected_dz.bed" <<EOF
 chr2	100	1
 chr2	101	1
 chr2	102	1
 EOF
-cat > "test_data/expected_strand.bed" <<EOF
+cat > "$TMPDIR/expected_strand.bed" <<EOF
 chr2	0	198295459	198295559	1
 chr2	1	100	198295559	5.04298e-07
 chr1	0	248956422	248956422	1
 chr3	0	242193529	242193529	1
 genome	0	689445410	689445510	1
 genome	1	100	689445510	1.45044e-07
 EOF
-cat > "test_data/expected_5.bed" <<EOF
+cat > "$TMPDIR/expected_5.bed" <<EOF
 chr2	0	198295557	198295559	1
 chr2	1	2	198295559	1.0086e-08
 chr1	0	248956422	248956422	1
 chr3	0	242193529	242193529	1
 genome	0	689445508	689445510	1
 genome	1	2	689445510	2.90088e-09
 EOF
-cat > "test_data/expected_bg_scale.bed" <<EOF
+cat > "$TMPDIR/expected_bg_scale.bed" <<EOF
 chr2	128	228	100
 chr2	428	528	100
 EOF
-cat > "test_data/expected_trackopts.bed" <<EOF
+cat > "$TMPDIR/expected_trackopts.bed" <<EOF
 track type=bedGraph name=example
 chr2	128	228	1
 chr2	428	528	1
 EOF
-cat > "test_data/expected_split.bed" <<EOF
+cat > "$TMPDIR/expected_split.bed" <<EOF
 chr2	0	198295359	198295559	0.999999
 chr2	1	200	198295559	1.0086e-06
 chr1	0	248956422	248956422	1
 chr3	0	242193529	242193529	1
 genome	0	689445310	689445510	1
 genome	1	200	689445510	2.90088e-07
 EOF
-cat > "test_data/expected_ignoreD_du.bed" <<EOF
+cat > "$TMPDIR/expected_ignoreD_du.bed" <<EOF
 chr2:172936693-172938111	0	1218	1418	0.858956
 chr2:172936693-172938111	1	200	1418	0.141044
 genome	0	1218	1418	0.858956
 genome	1	200	1418	0.141044
 EOF
 
 # Test 1: 
-mkdir test1
-cd test1
+mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null
 
 echo "> Run bedtools_genomecov on BED file"
 "$meta_executable" \
-  --input "../test_data/example.bed" \
-  --genome "../test_data/genome.txt" \
+  --input "../example.bed" \
+  --genome "../genome.txt" \
   --output "output.bed"
 
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_default.bed"
+assert_identical_content "output.bed" "../expected_default.bed"
 echo "- test1 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 2: ibam option 
-mkdir test2
-cd test2
+mkdir "$TMPDIR/test2" && pushd "$TMPDIR/test2" > /dev/null
 
 echo "> Run bedtools_genomecov on BAM file with -ibam"
 "$meta_executable" \
@@ -140,130 +142,123 @@ echo "> Run bedtools_genomecov on BAM file with -ibam"
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_ibam.bed"
+assert_identical_content "output.bed" "../expected_ibam.bed"
 echo "- test2 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 3: depth option
-mkdir test3
-cd test3
+mkdir "$TMPDIR/test3" && pushd "$TMPDIR/test3" > /dev/null
 
 echo "> Run bedtools_genomecov on BED file with -dz"
 "$meta_executable" \
-  --input "../test_data/example_dz.bed" \
-  --genome "../test_data/genome.txt" \
+  --input "../example_dz.bed" \
+  --genome "../genome.txt" \
   --output "output.bed" \
   --depth_zero
 
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_dz.bed"
+assert_identical_content "output.bed" "../expected_dz.bed"
 echo "- test3 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 4: strand option
-mkdir test4
-cd test4
+mkdir "$TMPDIR/test4" && pushd "$TMPDIR/test4" > /dev/null
 
 echo "> Run bedtools_genomecov on BED file with -strand"
 "$meta_executable" \
-  --input "../test_data/example.bed" \
-  --genome "../test_data/genome.txt" \
+  --input "../example.bed" \
+  --genome "../genome.txt" \
   --output "output.bed" \
   --strand "-" \
 
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_strand.bed"
+assert_identical_content "output.bed" "../expected_strand.bed"
 echo "- test4 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 5: 5' end option
-mkdir test5
-cd test5
+mkdir "$TMPDIR/test5" && pushd "$TMPDIR/test5" > /dev/null
 
 echo "> Run bedtools_genomecov on BED file with -5"
 "$meta_executable" \
-  --input "../test_data/example.bed" \
-  --genome "../test_data/genome.txt" \
+  --input "../example.bed" \
+  --genome "../genome.txt" \
   --output "output.bed" \
   --five_prime \
 
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_5.bed"
+assert_identical_content "output.bed" "../expected_5.bed"
 echo "- test5 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 6: max option
-mkdir test6
-cd test6
+mkdir "$TMPDIR/test6" && pushd "$TMPDIR/test6" > /dev/null
 
 echo "> Run bedtools_genomecov on BED file with -max"
 "$meta_executable" \
-  --input "../test_data/example.bed" \
-  --genome "../test_data/genome.txt" \
+  --input "../example.bed" \
+  --genome "../genome.txt" \
   --output "output.bed" \
   --max 100 \
 
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_default.bed"
+assert_identical_content "output.bed" "../expected_default.bed"
 echo "- test6 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 7: bedgraph and scale option
-mkdir test7
-cd test7
+mkdir "$TMPDIR/test7" && pushd "$TMPDIR/test7" > /dev/null
 
 echo "> Run bedtools_genomecov on BED file with -bg and -scale"
 "$meta_executable" \
-  --input "../test_data/example.bed" \
-  --genome "../test_data/genome.txt" \
+  --input "../example.bed" \
+  --genome "../genome.txt" \
   --output "output.bed" \
   --bed_graph \
   --scale 100 \
 
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_bg_scale.bed"
+assert_identical_content "output.bed" "../expected_bg_scale.bed"
 echo "- test7 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 8: trackopts option
-mkdir test8
-cd test8
+mkdir "$TMPDIR/test8" && pushd "$TMPDIR/test8" > /dev/null
 
 echo "> Run bedtools_genomecov on BED file with -bg and -trackopts"
 "$meta_executable" \
-  --input "../test_data/example.bed" \
-  --genome "../test_data/genome.txt" \
+  --input "../example.bed" \
+  --genome "../genome.txt" \
   --output "output.bed" \
   --bed_graph \
   --trackopts "name=example" \
 
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_trackopts.bed"
+assert_identical_content "output.bed" "../expected_trackopts.bed"
 echo "- test8 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 9: ibam pc options
-mkdir test9
-cd test9
+mkdir "$TMPDIR/test9" && pushd "$TMPDIR/test9" > /dev/null
 
 echo "> Run bedtools_genomecov on BAM file with -ibam, -pc"
 "$meta_executable" \
@@ -275,14 +270,13 @@ echo "> Run bedtools_genomecov on BAM file with -ibam, -pc"
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_ibam_pc.bed"
+assert_identical_content "output.bed" "../expected_ibam_pc.bed"
 echo "- test9 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 10: ibam fs options
-mkdir test10
-cd test10
+mkdir "$TMPDIR/test10" && pushd "$TMPDIR/test10" > /dev/null
 
 echo "> Run bedtools_genomecov on BAM file with -ibam, -fs"
 "$meta_executable" \
@@ -293,33 +287,31 @@ echo "> Run bedtools_genomecov on BAM file with -ibam, -fs"
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_ibam_fs.bed"
+assert_identical_content "output.bed" "../expected_ibam_fs.bed"
 echo "- test10 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 11: split 
-mkdir test11
-cd test11
+mkdir "$TMPDIR/test11" && pushd "$TMPDIR/test11" > /dev/null
 
 echo "> Run bedtools_genomecov on BED12 file with -split"
 "$meta_executable" \
-  --input "../test_data/example.bed12" \
-  --genome "../test_data/genome.txt" \
+  --input "../example.bed12" \
+  --genome "../genome.txt" \
   --output "output.bed" \
   --split \
 
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_split.bed"
+assert_identical_content "output.bed" "../expected_split.bed"
 echo "- test11 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 12: ignore deletion and du
-mkdir test12
-cd test12
+mkdir "$TMPDIR/test12" && pushd "$TMPDIR/test12" > /dev/null
 
 echo "> Run bedtools_genomecov on BAM file with -ignoreD and -du"
 "$meta_executable" \
@@ -331,10 +323,10 @@ echo "> Run bedtools_genomecov on BAM file with -ignoreD and -du"
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_ignoreD_du.bed"
+assert_identical_content "output.bed" "../expected_ignoreD_du.bed"
 echo "- test12 succeeded -"
 
-cd ..
+popd > /dev/null
 
 echo "---- All tests succeeded! ----"
 exit 0