update on test.sh

viash-hub · Aug 7, 2024 · bac80a5 · bac80a5
1 parent da6e11f
commit bac80a5
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Showing 3 changed files with 22 additions and 8 deletions.
diff --git a/src/bedtools/bedtools_genomecov/test.sh b/src/bedtools/bedtools_genomecov/test.sh
@@ -29,25 +29,34 @@ assert_identical_content() {
 echo "Creating Test Data..."
 mkdir -p test_data
 
-# create input files
-
-# create expected output files
+# 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"
 
 
 # Test 1: 
 mkdir test1
 cd test1
 
 echo "> Run bedtools_genomecov on BED file"
-# "$meta_executable" \
-#   --input_a "../test_data/featuresA.bed" \
-#   --input_b "../test_data/featuresB.bed" \
-#   --output "output.bed"
+"$meta_executable" \
+  --input "../test_data/example.bed" \
+  --genome "../test_data/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" "../test_data/expected_default.bed"
 echo "- test1 succeeded -"
 
 cd ..

diff --git a/src/bedtools/bedtools_genomecov/test_data/example.bed b/src/bedtools/bedtools_genomecov/test_data/example.bed
@@ -0,0 +1,2 @@
+chr2	128	228	my_read/1	37	+
+chr2	428	528	my_read/2	37	-
diff --git a/src/bedtools/bedtools_genomecov/test_data/genome.txt b/src/bedtools/bedtools_genomecov/test_data/genome.txt
@@ -0,0 +1,3 @@
+chr1	248956422
+chr2	198295559
+chr3	242193529
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		chr2 128 228 my_read/1 37 +
		chr2 428 528 my_read/2 37 -