all test implemented

src/bedtools/bedtools_merge/config.vsh.yaml

@@ -61,12 +61,11 @@ argument_groups:
 
       - name: --columns
         alternatives: -c
-        type: integer
+        type: string
         description: | 
           Specify columns from the B file to map onto intervals in A.
           Default: 5.
           Multiple columns can be specified in a comma-delimited list.
-      # maybe type is string??? ask tomorrow!
 
       - name: --operation
         alternatives: -o
@@ -103,8 +102,8 @@ argument_groups:
         type: string
         description: | 
           Specify a custom delimiter for the collapse operations.
-          - Example: -delim "|"
-          - Default: ",".
+        example: "|"
+        default: ","
 
       - name: --precision
         alternatives: -prec

src/bedtools/bedtools_merge/script.sh

@@ -19,7 +19,7 @@ bedtools merge \
     ${par_distance:+-d "$par_distance"} \
     ${par_columns:+-c "$par_columns"} \
     ${par_operation:+-o "$par_operation"} \
-    ${par_delimeter:+-delim "$par_delimeter"} \
+    ${par_delimiter:+-delim "$par_delimiter"} \
     ${par_precision:+-prec "$par_precision"} \
     -i "$par_input" \
     > "$par_output"

src/bedtools/bedtools_merge/test.sh

@@ -35,21 +35,27 @@ mkdir -p test_data
 # Create and populate example files
 printf "chr1\t100\t200\nchr1\t150\t250\nchr1\t300\t400\n" > "test_data/featureA.bed"
 printf "chr1\t100\t200\ta1\t1\t+\nchr1\t180\t250\ta2\t2\t+\nchr1\t250\t500\ta3\t3\t-\nchr1\t501\t1000\ta4\t4\t+\n" > "test_data/featureB.bed"
+printf "chr1\t100\t200\ta1\t1.9\t+\nchr1\t180\t250\ta2\t2.5\t+\nchr1\t250\t500\ta3\t3.3\t-\nchr1\t501\t1000\ta4\t4\t+\n" > "test_data/feature_precision.bed"
 
-# Create and populate example.gff file
-printf "chr1\t.\tgene\t1000\t2000\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/expected_sorted.gff"
-printf "chr1\t.\texon\t1000\t1200\t.\t+\t.\tID=exon1;Parent=transcript1\n" >> "test_data/expected_sorted.gff"
-printf "chr1\t.\tCDS\t1000\t1200\t.\t+\t0\tID=cds1;Parent=transcript1\n" >> "test_data/expected_sorted.gff"
-printf "chr1\t.\tCDS\t1500\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/expected_sorted.gff"
-printf "chr2\t.\texon\t1500\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/expected_sorted.gff"
-printf "chr3\t.\tmRNA\t1000\t2000\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/expected_sorted.gff"
+# Create and populate feature.gff file
+printf "##gff-version 3\n" > "test_data/feature.gff"
+printf "chr1\t.\tgene\t1000\t2000\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/feature.gff"
+printf "chr1\t.\texon\t1000\t1200\t.\t+\t.\tID=exon1;Parent=transcript1\n" >> "test_data/feature.gff"
+printf "chr1\t.\tCDS\t1000\t1200\t.\t+\t0\tID=cds1;Parent=transcript1\n" >> "test_data/feature.gff"
+printf "chr1\t.\tCDS\t1500\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/feature.gff"
+printf "chr2\t.\texon\t1500\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/feature.gff"
+printf "chr3\t.\tmRNA\t1000\t2000\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/feature.gff"
 
 # Create expected output files
 printf "chr1\t100\t250\nchr1\t300\t400\n" > "test_data/expected.bed"
 printf "chr1\t100\t250\nchr1\t250\t500\nchr1\t501\t1000\n" > "test_data/expected_strand.bed"
 printf "chr1\t100\t250\nchr1\t501\t1000\n" > "test_data/expected_specific_strand.bed"
 printf "chr1\t128\t228\nchr1\t428\t528\n" > "test_data/expected_bam.bed"
 printf "chr1\t100\t400\n" > "test_data/expected_distance.bed"
+printf "chr1\t100\t500\t2\t1\t3\nchr1\t501\t1000\t4\t4\t4\n" > "test_data/expected_operation.bed"
+printf "chr1\t100\t500\ta1|a2|a3\nchr1\t501\t1000\ta4\n" > "test_data/expected_delim.bed"
+printf "chr1\t100\t500\t2.567\nchr1\t501\t1000\t4\n" > "test_data/expected_precision.bed"
+printf "##gff-version 3\nchr1\t999\t2000\nchr2\t1499\t1700\nchr3\t999\t2000\n" > "test_data/expected_header.bed"
 
 # Test 1: Default sort on BED file
 mkdir test1
@@ -140,24 +146,82 @@ echo "- test5 succeeded -"
 
 cd ..
 
-# Test 6: columns option
-# mkdir test6
-# cd test6
+# Test 6: columns option & operation option
+mkdir test6
+cd test6
 
-# echo "> Run bedtools_merge on BED file with columns option"
-# "$meta_executable" \
-#   --input "../test_data/featureA.bed" \
-#   --output "output.bed" \
-#   --columns 2
+echo "> Run bedtools_merge on BED file with columns & operation options"
+"$meta_executable" \
+  --input "../test_data/featureB.bed" \
+  --output "output.bed" \
+  --columns 5 \
+  --operation "mean,min,max"
 
-# # checks
-# assert_file_exists "output.bed"
-# assert_file_not_empty "output.bed"
-# assert_identical_content "output.bed" "../test_data/expected.bed"
-# echo "- test6 succeeded -"
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_operation.bed"
+echo "- test6 succeeded -"
+
+cd ..
 
-# cd ..
+# Test 8: delimeter option
+mkdir test8
+cd test8
 
+echo "> Run bedtools_merge on BED file with delimeter option"
+"$meta_executable" \
+  --input "../test_data/featureB.bed" \
+  --output "output.bed" \
+  --columns 4 \
+  --operation "collapse" \
+  --delimiter "|"
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_delim.bed"
+echo "- test8 succeeded -"
+
+cd ..
+
+# Test 9: precision option
+mkdir test9
+cd test9
+
+echo "> Run bedtools_merge on BED file with precision option"
+"$meta_executable" \
+  --input "../test_data/feature_precision.bed" \
+  --output "output.bed" \
+  --columns 5 \
+  --operation "mean" \
+  --precision 4
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_precision.bed"
+echo "- test9 succeeded -"
+
+cd ..
+
+# Test 10: header option
+mkdir test10
+cd test10
+
+echo "> Run bedtools_merge on GFF file with header option"
+"$meta_executable" \
+  --input "../test_data/feature.gff" \
+  --output "output.gff" \
+  --header
+
+# checks
+assert_file_exists "output.gff"
+assert_file_not_empty "output.gff"
+assert_identical_content "output.gff" "../test_data/expected_header.bed"
+echo "- test10 succeeded -"
+
+cd ..
 
 echo "---- All tests succeeded! ----"
 exit 0