Refined tests

src/gffread/config.vsh.yaml

@@ -85,10 +85,11 @@ argument_groups:
       - name: --spliced_exons
         alternatives: -w
         type: file
+        direction: output
         must_exist: false
-        example: exons.fa
         description: |
           Write a fasta file with spliced exons for each transcript.
+        example: exons.fa
       - name: --w_add
         type: integer
         description: |

src/gffread/script.sh

@@ -7,10 +7,12 @@
 [[ "$par_coding" == "false" ]] && unset par_coding
 [[ "$par_strict_range" == "false" ]] && unset par_strict_range
 [[ "$par_no_single_exon" == "false" ]] && unset par_no_single_exon
+[[ "$par_no_exon_attrs" == "false" ]] && unset par_no_exon_attrs
 [[ "$par_nc" == "false" ]] && unset par_nc
 [[ "$par_ignore_locus" == "false" ]] && unset par_ignore_locus
 [[ "$par_description" == "false" ]] && unset par_description
 [[ "$par_sort_alpha" == "false" ]] && unset par_sort_alpha
+[[ "$par_keep_genes" == "false" ]] && unset par_keep_genes
 [[ "$par_keep_attrs" == "false" ]] && unset par_keep_attrs
 [[ "$par_keep_exon_attrs" == "false" ]] && unset par_keep_exon_attrs
 [[ "$par_keep_comments" == "false" ]] && unset par_keep_comments
@@ -61,7 +63,7 @@ gffread \
     ${par_merge_exons:+-Z} \
     ${par_genome:+-g "$par_genome"} \
     ${par_junctions:+-j} \
-    ${par_spliced_exons:+-w "$par_spliced_exon"} \
+    ${par_spliced_exons:+-w "$par_spliced_exons"} \
     ${par_w_add:+--w-add "$par_w_add"} \
     ${par_w_nocds:+--w-nocds} \
     ${par_spliced_cds:+-x "$par_spliced_cds"} \

src/gffread/test.sh

@@ -5,19 +5,21 @@
 
 set -e
 
-test_output_dir="$meta_resources_dir/test_data/test_output/"
-test_dir="$meta_resources_dir/test_data/"
-expected_output_dir="$meta_resources_dir/test_data/output/"
+test_output_dir="${meta_resources_dir}test_data/test_output"
+test_dir="${meta_resources_dir}test_data"
+expected_output_dir="${meta_resources_dir}test_data/output"
+
+mkdir -p "$test_output_dir"
 
 
 ################################################################################
 
 echo "> Test 1 - Read annotation file, output GFF" 
 
 "$meta_executable" \
-  --expose_dups \
-  --outfile "$test_output_dir/ann_simple.gff" \
-  --input "$test_dir/annotation.gff"
+  -E \
+  --input "$test_dir/annotation.gff" \
+  -o "$test_output_dir/ann_simple.gff" 
 
 echo ">> Check if output exists"
 [ ! -f "$test_output_dir/ann_simple.gff" ] \
@@ -28,9 +30,14 @@ echo ">> Check if output is empty"
     && echo "Output file test_output/ann_simple.gff is empty" && exit 1
 
 echo ">> Compare output to expected output"
-diff "$expected_output_dir/ann_simple.gff" "$test_output_dir/ann_simple.gff" || \
+
+# Not comparing header lines, they are not in the same order and reference file
+# was created with a different version of gffread.
+diff <(grep -v '^#' "$expected_output_dir/ann_simple.gff") \
+    <(grep -v '^#' "$test_output_dir/ann_simple.gff") || \
     (echo "Output file ann_simple.gff does not match expected output" && exit 1)
 
+
 ################################################################################
 
 echo "> Test 2 - Read annotation file, output GTF"
@@ -49,25 +56,33 @@ echo ">> Check if output is empty"
     && echo "Output file test_output/annotation.gtf is empty" && exit 1
 
 echo ">> Compare output to expected output"
+
+# remove trailing semicolons from the files
+# Difference in trailing semicolon presence might be due to reference output 
+# being generated by gffred version 11.8 instead of 12.7.
+sed -i 's/;$/''/' "$expected_output_dir/annotation.gtf"
+sed -i 's/;$/''/' "$test_output_dir/annotation.gtf"
+
 diff "$expected_output_dir/annotation.gtf" "$test_output_dir/annotation.gtf" || \
     (echo "Output file annotation.gtf does not match expected output" && exit 1)
 
 ################################################################################
 
 echo "> Test 3 - Generate fasta file from annotation file"
 
+
 "$meta_executable" \
+  --genome "$test_dir/genome.fa" \
   --spliced_exons "$test_output_dir/transcripts.fa" \
-  --genome "genome.fa" \
-  --input "annotation.gff"
+  --input "$test_dir/annotation.gff"
 
 echo ">> Check if output exists"
 [ ! -f "$test_output_dir/transcripts.fa" ] \
-    && echo "Output file test_output/transcripts.fa does not exist" && exit 1
+    && echo "Output file transcripts.fa does not exist" && exit 1
 
 echo ">> Check if output is empty"
 [ ! -s "$test_output_dir/transcripts.fa" ] \
-    && echo "Output file test_output/transcripts.fa is empty" && exit 1
+    && echo "Output file transcripts.fa is empty" && exit 1
 
 echo ">> Compare output to expected output"
 diff "$expected_output_dir/transcripts.fa" "$test_output_dir/transcripts.fa" || \
@@ -80,7 +95,7 @@ echo "> Test 4 - Generate table from GFF annotation file"
 "$meta_executable" \
   --table @id,@chr,@start,@end,@strand,@exons,Name,gene,product \
   --outfile "$test_output_dir/annotation.tbl" \
-  --input "annotation.gff"
+  --input "$test_dir/annotation.gff"
 
 echo ">> Check if output exists"
 [ ! -f "$test_output_dir/annotation.tbl" ] \
@@ -94,6 +109,9 @@ echo ">> Compare output to expected output"
 diff "$expected_output_dir/annotation.tbl" "$test_output_dir/annotation.tbl" || \
     (echo "Output file annotation.tbl does not match expected output" && exit 1)
 
+# reference output annotation.tbl was created manually since it was not included
+# in the original test data.
+
 ################################################################################
 
 echo "> All tests successful"

src/gffread/test_data/output/annotation.tbl

@@ -0,0 +1,4 @@
+rna157470	NT_187562.1	411	68627	+	411-495,1995-2051,2602-2726,9665-9753,12115-12164,12577-12744,14174-14326,14664-14864,16634-16788,17438-17606,17880-17976,18710-18822,20083-20208,21352-21480,21736-21846,22191-22253,24448-24582,25379-25466,26264-26402,27215-27348,56500-56534,56627-56743,57445-57593,58211-58295,59473-59529,61493-61617,62682-62770,64510-64559,65149-65319,67694-68627	NM_004668.2	MGAM	maltase-glucoamylase
+rna157473	NT_187562.1	214038	219958	-	214038-214270,214372-214511,216955-217211,217435-217573,219568-219648,219891-219958	NM_001001317.4	PRSS58	protease%2C serine 58
+rna157474	NT_187562.1	230181	234148	-	230181-231784,233047-233200,233852-234148	NR_036483.2	TRY2P	trypsinogen-like pseudogene
+rna157497	NT_187562.1	962573	963937	+	962573-962821,963419-963937	NM_178829.4	C7orf34	chromosome 7 open reading frame 34