tests extended

src/seqtk/seqtk_sample/test.sh

@@ -11,7 +11,7 @@ meta_resources_dir="src/seqtk/seqtk_sample"
 mkdir seqtk_sample_se
 cd seqtk_sample_se
 
-echo "> Run seqtk_sample on SE with fastq"
+echo "> Run seqtk_sample on fastq SE"
 "$meta_executable" \
   --input "$meta_resources_dir/test_data/reads/a.fastq" \
   --seed 42 \
@@ -24,14 +24,12 @@ if [ ! -f "sampled.fastq" ]; then
     exit 1
 fi
 
-cat sampled.fastq
-
 #########################################################################################
 cd ..
-mkdir seqtk_sample_pe
-cd seqtk_sample_pe
+mkdir seqtk_sample_pe_number
+cd seqtk_sample_pe_number
 
-echo ">> Run seqtk_sample on PE with fastq.gz"
+echo ">> Run seqtk_sample on fastq.gz PE with number of reads"
 "$meta_executable" \
   --input "$meta_resources_dir/test_data/reads/a.1.fastq.gz" \
   --seed 42 \
@@ -56,4 +54,37 @@ headers1=$(grep '^@' sampled_1.fastq | sed -e's/ 1$//' | sort)
 headers2=$(grep '^@' sampled_2.fastq | sed -e 's/ 2$//' | sort)
 
 # Compare headers
-diff <(echo "$headers1") <(echo "$headers2") || echo "Mismatch detected" && exit 1
+diff <(echo "$headers1") <(echo "$headers2") || { echo "Mismatch detected"; exit 1; }
+
+#########################################################################################
+cd ..
+mkdir seqtk_sample_pe_fraction
+cd seqtk_sample_pe_fraction
+
+echo ">> Run seqtk_sample on fastq.gz PE with fraction of reads"
+"$meta_executable" \
+  --input "$meta_resources_dir/test_data/reads/a.1.fastq.gz" \
+  --seed 42 \
+  --fraction_number 0.5 \
+  --output "sampled_1.fastq"
+
+"$meta_executable" \
+  --input "$meta_resources_dir/test_data/reads/a.2.fastq.gz" \
+  --seed 42 \
+  --fraction_number 0.5 \
+  --output "sampled_2.fastq"
+
+echo ">> Check if output exists"
+if [ ! -f "sampled_1.fastq" ] || [ ! -f "sampled_2.fastq" ]; then
+    echo ">> One or both output files do not exist"
+    exit 1
+fi
+
+echo ">> Compare reads"
+# Extract headers
+headers1=$(grep '^@' sampled_1.fastq | sed -e's/ 1$//' | sort)
+headers2=$(grep '^@' sampled_2.fastq | sed -e 's/ 2$//' | sort)
+
+# Compare headers
+diff <(echo "$headers1") <(echo "$headers2") || { echo "Mismatch detected"; exit 1; }
+