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authorPeter Amstutz2020-07-07 15:52:46 -0400
committerPeter Amstutz2020-07-07 15:55:06 -0400
commit7cf561c1b92a44d488d36dd3d883750b261c6550 (patch)
treebdcc34b45f0dd31dfcb15d44c4049ec9ea46b51f /bh20sequploader/qc_fasta.py
parent4f30e506055acb788a1ff1bbcb6359c4413a4eab (diff)
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Use minimap2 instead of clustalw for fasta QC
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'bh20sequploader/qc_fasta.py')
-rw-r--r--bh20sequploader/qc_fasta.py61
1 files changed, 26 insertions, 35 deletions
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":