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authorlltommy2020-07-07 23:58:50 +0200
committerlltommy2020-07-07 23:58:50 +0200
commitc8ffc952a99dc0a2d1266cdc0636711ec63e8bfb (patch)
treed8672cca90c8469f07c20cb80fdbf0439913623a /bh20sequploader/qc_fasta.py
parent027d7bd6dd89c62a1e81bbda0e6ef7f27cbb3920 (diff)
parentb994b59963248a301e1248f792f21d9ab2ea8a3f (diff)
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Merge branch 'master' of https://github.com/arvados/bh20-seq-resource
Diffstat (limited to 'bh20sequploader/qc_fasta.py')
-rw-r--r--bh20sequploader/qc_fasta.py73
1 files changed, 37 insertions, 36 deletions
diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py
index e198430..37eb4e8 100644
--- a/bh20sequploader/qc_fasta.py
+++ b/bh20sequploader/qc_fasta.py
@@ -25,7 +25,7 @@ def read_fasta(sequence):
raise ValueError("FASTA file contains multiple entries")
return label, bases
-def qc_fasta(arg_sequence):
+def qc_fasta(arg_sequence, check_with_clustalw=True):
log.debug("Starting qc_fasta")
schema_resource = pkg_resources.resource_stream(__name__, "validation/formats")
with tempfile.NamedTemporaryFile() as tmp:
@@ -51,47 +51,48 @@ def qc_fasta(arg_sequence):
if seq_type == "text/fasta":
# ensure that contains only one entry
submitlabel, submitseq = read_fasta(sequence)
+ sequence.seek(0)
+ sequence.detach()
- 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))
+ if not check_with_clustalw:
+ return ("sequence.fasta"+gz, seqlabel)
- print(g1.group(0))
- print(g2.group(0))
- print(g3.group(0))
- except Exception as e:
- logging.warn("Error trying to QC against reference sequence using 'clustalw': %s", e)
+ with tempfile.NamedTemporaryFile() as tmp1:
+ 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]
+ logging.info("QC checking similarity to reference")
+ logging.info(" ".join(cmd))
+ result = subprocess.run(cmd, stdout=subprocess.PIPE)
+ result.check_returncode()
+ res = result.stdout.decode("utf-8")
+ mm = res.split("\t")
+ if len(mm) >= 10:
+ # divide Number of matching bases in the mapping / Target sequence length
+ similarity = (float(mm[9]) / float(mm[6])) * 100.0
+ else:
+ similarity = 0
+ except Exception as e:
+ logging.warn("QC against reference sequence using 'minimap2': %s", e, exc_info=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":
+ sequence.seek(0)
+ sequence.detach()
return ("reads.fastq"+gz, seqlabel)
else:
raise ValueError("Sequence file does not look like a DNA FASTA or FASTQ")