1 files changed, 63 insertions, 0 deletions
diff --git a/workflows/yamlfa2ttl/check_sequence.py b/workflows/yamlfa2ttl/check_sequence.py
new file mode 100644
index 0000000..f92bf6d
--- /dev/null
+++ b/workflows/yamlfa2ttl/check_sequence.py
@@ -0,0 +1,63 @@
+import subprocess
+import tempfile
+import sys
+
+path_fasta = sys.argv[1]
+path_sars_cov_2_reference_fasta = sys.argv[2]
+
+
+def read_single_fasta(path_fasta):
+    with open(path_fasta) as f:
+        entries = 0
+        header = None
+        sequence = []
+        for line in f:
+            line = line.strip()
+
+            if line.startswith(">"):
+                header = line
+                entries += 1
+            else:
+                sequence.append(line)
+
+            if entries > 1:
+                raise ValueError("Input FASTA contains multiple entries")
+
+    return header, ''.join(sequence)
+
+
+print("FASTA QC: checking similarity to the reference")
+
+header, sequence = read_single_fasta(path_fasta)
+
+similarity = 0
+
+with tempfile.NamedTemporaryFile() as tmp_fasta:
+    with tempfile.NamedTemporaryFile() as tmp_sars_cov_2_reference_fasta:
+        with open(path_sars_cov_2_reference_fasta, 'rb') as f:
+            tmp_sars_cov_2_reference_fasta.write(f.read())
+        tmp_sars_cov_2_reference_fasta.flush()
+
+        tmp_fasta.write(f'>{header}\n'.encode("utf8"))
+        tmp_fasta.write(sequence.encode("utf8"))
+        tmp_fasta.flush()
+
+        cmd = [
+            "minimap2", "-c", "-x", "asm20",
+            tmp_sars_cov_2_reference_fasta.name, tmp_fasta.name
+        ]
+        print(" ".join(cmd))
+
+        result = subprocess.run(cmd, stdout=subprocess.PIPE)
+        result.check_returncode()
+
+        paf_output = result.stdout.decode("utf-8")
+        paf_output = paf_output.split("\t")
+        if len(paf_output) >= 10:
+            # Number of matching bases in the mapping / Target sequence length
+            similarity = (float(paf_output[9]) / float(paf_output[6])) * 100.0
+
+if similarity < 70.0:
+    raise ValueError(
+        f"FASTA QC fail for '{header}': the similarity against the reference {similarity} was less than 70%')"
+    )