From 7cf561c1b92a44d488d36dd3d883750b261c6550 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Tue, 7 Jul 2020 15:52:46 -0400
Subject: Use minimap2 instead of clustalw for fasta QC

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 bh20sequploader/main.py     |  9 +++++--
 bh20sequploader/qc_fasta.py | 61 +++++++++++++++++++--------------------------
 2 files changed, 33 insertions(+), 37 deletions(-)

diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 8555e2b..fd0278d 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -23,14 +23,16 @@ ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
 UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa'
 
 def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True):
+    failed = False
     try:
         log.debug("Checking metadata" if do_qc else "Skipping metadata check")
         if do_qc and not qc_metadata(metadata.name):
-            raise Exception("Failed metadata qc")
+            log.warning("Failed metadata qc")
+            failed = True
     except Exception as e:
         log.debug(e)
         print(e)
-        exit(1)
+        failed = True
 
     target = []
     try:
@@ -43,6 +45,9 @@ def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True):
     except Exception as e:
         log.debug(e)
         print(e)
+        failed = True
+
+    if failed:
         exit(1)
 
     return target
diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py
index 8c6ebd3..b08333e 100644
--- a/bh20sequploader/qc_fasta.py
+++ b/bh20sequploader/qc_fasta.py
@@ -58,42 +58,33 @@ def qc_fasta(arg_sequence, check_with_clustalw=True):
             return ("sequence.fasta"+gz, seqlabel)
 
         with tempfile.NamedTemporaryFile() as tmp1:
-            refstring = pkg_resources.resource_string(__name__, "SARS-CoV-2-reference.fasta")
-            tmp1.write(refstring)
-            tmp1.write(submitlabel.encode("utf8"))
-            tmp1.write(("".join(submitseq)).encode("utf8"))
-            tmp1.flush()
-            subbp = 0
-            refbp = 0
-            similarity = 0
-            try:
-                cmd = ["clustalw", "-infile="+tmp1.name,
-                       "-quicktree", "-iteration=none", "-type=DNA"]
-                print("QC checking similarity to reference")
-                print(" ".join(cmd))
-                result = subprocess.run(cmd, stdout=subprocess.PIPE)
-                res = result.stdout.decode("utf-8")
-                g1 = re.search(r"^Sequence 1: [^ ]+ +(\d+) bp$", res, flags=re.MULTILINE)
-                refbp = float(g1.group(1))
-                g2 = re.search(r"^Sequence 2: [^ ]+ +(\d+) bp$", res, flags=re.MULTILINE)
-                subbp = float(g2.group(1))
-                g3 = re.search(r"^Sequences \(1:2\) Aligned\. Score: (\d+(\.\d+)?)$", res, flags=re.MULTILINE)
-                similarity = float(g3.group(1))
+            with tempfile.NamedTemporaryFile() as tmp2:
+                refstring = pkg_resources.resource_string(__name__, "SARS-CoV-2-reference.fasta")
+                tmp1.write(refstring)
+                tmp1.flush()
+                tmp2.write(submitlabel.encode("utf8"))
+                tmp2.write(("".join(submitseq)).encode("utf8"))
+                tmp2.flush()
+                subbp = 0
+                refbp = 0
+                similarity = 0
+                try:
+                    cmd = ["minimap2", "-c", tmp1.name, tmp2.name]
+                    print("QC checking similarity to reference")
+                    print(" ".join(cmd))
+                    result = subprocess.run(cmd, stdout=subprocess.PIPE)
+                    res = result.stdout.decode("utf-8")
+                    mm = res.split("\t")
+                    print(mm)
+                    # divide Number of matching bases in the mapping / Target sequence length
+                    similarity = (float(mm[9]) / float(mm[6])) * 100.0
+                except Exception as e:
+                    logging.warn("QC against reference sequence using 'minimap2': %s", e)
 
-                print(g1.group(0))
-                print(g2.group(0))
-                print(g3.group(0))
-            except Exception as e:
-                logging.warn("QC against reference sequence using 'clustalw': %s", e)
-
-            if refbp and (subbp/refbp) < .7:
-                raise ValueError("QC fail: submit sequence length is shorter than 70% reference")
-            if refbp and (subbp/refbp) > 1.3:
-                raise ValueError("QC fail: submit sequence length is greater than 130% reference")
-            if similarity and similarity < 70.0:
-                raise ValueError("QC fail: submit similarity is less than 70%")
-            if refbp == 0 or similarity == 0:
-                raise ValueError("QC fail")
+                if similarity and similarity < 70.0:
+                    raise ValueError("QC fail: alignment to reference was less than 70%% (was %2.2f%%)" % (similarity))
+                if similarity == 0:
+                    raise ValueError("QC fail")
 
         return ("sequence.fasta"+gz, seqlabel)
     elif seq_type == "text/fastq":
-- 
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