adding some tests

src/bedtools/bedtools_groupby/config.vsh.yaml

@@ -83,7 +83,6 @@ argument_groups:
           E.g., "-c 5,4,6 -o sum,mean,count" will give the sum of column 5,
           the mean of column 4, and the count of column 6.
           The order of output columns will match the ordering given in the command.
-        required: true
 
       - name: --full
         type: boolean_true

src/bedtools/bedtools_groupby/script.sh

@@ -21,6 +21,6 @@ bedtools groupby \
     -i "$par_input" \
     -g "$par_groupby" \
     -c "$par_column" \
-    -o "$par_operation" \
+    ${par_operation:+-o "$par_operation"} \
     > "$par_output"
 

src/bedtools/bedtools_groupby/test.sh

@@ -29,28 +29,81 @@ assert_identical_content() {
 echo "Creating Test Data..."
 mkdir -p test_data
 
-# Create and populate featuresA.bed
+# Create and populate example.bed
+cat << EOF > test_data/example.bed
+# Header
+chr21	9719758	9729320	variant1	chr21	9719768	9721892	ALR/Alpha	1004	+
+chr21	9719758	9729320	variant1	chr21	9721905	9725582	ALR/Alpha	1010	+
+chr21	9719758	9729320	variant1	chr21	9725582	9725977	L1PA3	3288	+
+chr21	9719758	9729320	variant1	chr21	9726021	9729309	ALR/Alpha	1051	+
+chr21	9729310	9757478	variant2	chr21	9729320	9729809	L1PA3	3897	-
+chr21	9729310	9757478	variant2	chr21	9729809	9730866	L1P1	8367	+
+chr21	9729310	9757478	variant2	chr21	9730866	9734026	ALR/Alpha	1036	-
+chr21	9729310	9757478	variant2	chr21	9734037	9757471	ALR/Alpha	1182	-
+chr21	9795588	9796685	variant3	chr21	9795589	9795713	(GAATG)n	308	+
+chr21	9795588	9796685	variant3	chr21	9795736	9795894	(GAATG)n	683	+
+chr21	9795588	9796685	variant3	chr21	9795911	9796007	(GAATG)n	345	+
+chr21	9795588	9796685	variant3	chr21	9796028	9796187	(GAATG)n	756	+
+chr21	9795588	9796685	variant3	chr21	9796202	9796615	(GAATG)n	891	+
+chr21	9795588	9796685	variant3	chr21	9796637	9796824	(GAATG)n	621	+
+EOF
 
 # Create and populate expected output files for different tests
+cat << EOF > test_data/expected.bed
+chr21	9719758	9729320	6353
+chr21	9729310	9757478	14482
+chr21	9795588	9796685	3604
+EOF
+cat << EOF > test_data/expected_max.bed
+chr21	9719758	9729320	variant1	3288
+chr21	9729310	9757478	variant2	8367
+chr21	9795588	9796685	variant3	891
+EOF
 
-# Test 1: Default intersect
+# Test 1: without operation option, default operation is sum
 mkdir test1
 cd test1
 
-# echo "> Run bedtools_intersect on BED files with default intersect"
-# "$meta_executable" \
-#   --input_a "../test_data/featuresA.bed" \
-#   --input_b "../test_data/featuresB.bed" \
-#   --output "output.bed"
+echo "> Run bedtools groupby on BED file"
+"$meta_executable" \
+  --input "../test_data/example.bed" \
+  --groupby "1,2,3" \
+  --column "9" \
+  --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.bed"
 echo "- test1 succeeded -"
 
 cd ..
 
+# Test 2: with operation option
+mkdir test2
+cd test2
+
+echo "> Run bedtools groupby on BED file with max operation"
+"$meta_executable" \
+  --input "../test_data/example.bed" \
+  --groupby "1-4" \
+  --column "9" \
+  --operation "max" \
+  --output "output.bed"
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_max.bed"
+echo "- test2 succeeded -"
+
+cd ..
+
+# Test 3: 
+
+
+
+
 
 
 echo "---- All tests succeeded! ----"

src/bedtools/bedtools_groupby/test_data/example.bed

@@ -0,0 +1,15 @@
+# Header
+chr21	9719758	9729320	variant1	chr21	9719768	9721892	ALR/Alpha	1004	+
+chr21	9719758	9729320	variant1	chr21	9721905	9725582	ALR/Alpha	1010	+
+chr21	9719758	9729320	variant1	chr21	9725582	9725977	L1PA3	3288	+
+chr21	9719758	9729320	variant1	chr21	9726021	9729309	ALR/Alpha	1051	+
+chr21	9729310	9757478	variant2	chr21	9729320	9729809	L1PA3	3897	-
+chr21	9729310	9757478	variant2	chr21	9729809	9730866	L1P1	8367	+
+chr21	9729310	9757478	variant2	chr21	9730866	9734026	ALR/Alpha	1036	-
+chr21	9729310	9757478	variant2	chr21	9734037	9757471	ALR/Alpha	1182	-
+chr21	9795588	9796685	variant3	chr21	9795589	9795713	(GAATG)n	308	+
+chr21	9795588	9796685	variant3	chr21	9795736	9795894	(GAATG)n	683	+
+chr21	9795588	9796685	variant3	chr21	9795911	9796007	(GAATG)n	345	+
+chr21	9795588	9796685	variant3	chr21	9796028	9796187	(GAATG)n	756	+
+chr21	9795588	9796685	variant3	chr21	9796202	9796615	(GAATG)n	891	+
+chr21	9795588	9796685	variant3	chr21	9796637	9796824	(GAATG)n	621	+

src/bedtools/bedtools_groupby/test_data/expected.bed

@@ -0,0 +1,3 @@
+chr21	9719758	9729320	6353
+chr21	9729310	9757478	14482
+chr21	9795588	9796685	3604