From 141e619929cee17018417d71111063015e73c366 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Thu, 7 Jan 2021 23:02:54 +0100
Subject: added check_sequence workflow and script

---
 workflows/yamlfa2ttl/check_format.cwl   |  3 +-
 workflows/yamlfa2ttl/check_sequence.cwl | 20 +++++++++++
 workflows/yamlfa2ttl/check_sequence.py  | 63 +++++++++++++++++++++++++++++++++
 workflows/yamlfa2ttl/yamlfa2ttl.cwl     |  8 +++++
 4 files changed, 93 insertions(+), 1 deletion(-)
 create mode 100644 workflows/yamlfa2ttl/check_sequence.cwl
 create mode 100644 workflows/yamlfa2ttl/check_sequence.py

diff --git a/workflows/yamlfa2ttl/check_format.cwl b/workflows/yamlfa2ttl/check_format.cwl
index 24de620..9eee58a 100644
--- a/workflows/yamlfa2ttl/check_format.cwl
+++ b/workflows/yamlfa2ttl/check_format.cwl
@@ -3,6 +3,7 @@
 cwlVersion: v1.1
 class: CommandLineTool
 baseCommand: python3
+
 inputs:
   script:
     type: File
@@ -18,5 +19,5 @@ inputs:
     type: File
     inputBinding: {position: 4}
     default: {class: File, location: ../../bh20sequploader/validation/formats}
-outputs: []
 
+outputs: []
diff --git a/workflows/yamlfa2ttl/check_sequence.cwl b/workflows/yamlfa2ttl/check_sequence.cwl
new file mode 100644
index 0000000..946948d
--- /dev/null
+++ b/workflows/yamlfa2ttl/check_sequence.cwl
@@ -0,0 +1,20 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.1
+class: CommandLineTool
+baseCommand: python3
+
+inputs:
+  script:
+    type: File
+    inputBinding: {position: 1}
+    default: {class: File, location: check_sequence.py}
+  path_fasta:
+    type: string
+    inputBinding: {position: 2}
+  path_sars_cov_2_reference_fasta:
+    type: File
+    inputBinding: {position: 3}
+    default: {class: File, location: ../../bh20sequploader/SARS-CoV-2-reference.fasta}
+
+outputs: []
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%')"
+    )
diff --git a/workflows/yamlfa2ttl/yamlfa2ttl.cwl b/workflows/yamlfa2ttl/yamlfa2ttl.cwl
index 1dce9ca..143fc9d 100644
--- a/workflows/yamlfa2ttl/yamlfa2ttl.cwl
+++ b/workflows/yamlfa2ttl/yamlfa2ttl.cwl
@@ -18,7 +18,15 @@ steps:
     in:
       path_fasta: path_fasta
       format_to_check: format_to_check
+    doc: the input has to be a valid FASTA format file
     out: []
     run: check_format.cwl
 
+  check_sequence:
+    in:
+      path_fasta: path_fasta
+    doc: the input sequence has to be enough similar to the reference
+    out: []
+    run: check_sequence.cwl
+
 outputs: []
-- 
cgit v1.2.3