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-rw-r--r--bh20sequploader/qc_fasta.py15
-rw-r--r--scripts/docker/Dockerfile2
2 files changed, 10 insertions, 7 deletions
diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py
index b08333e..37eb4e8 100644
--- a/bh20sequploader/qc_fasta.py
+++ b/bh20sequploader/qc_fasta.py
@@ -70,16 +70,19 @@ def qc_fasta(arg_sequence, check_with_clustalw=True):
similarity = 0
try:
cmd = ["minimap2", "-c", tmp1.name, tmp2.name]
- print("QC checking similarity to reference")
- print(" ".join(cmd))
+ 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")
- print(mm)
- # divide Number of matching bases in the mapping / Target sequence length
- similarity = (float(mm[9]) / float(mm[6])) * 100.0
+ 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)
+ logging.warn("QC against reference sequence using 'minimap2': %s", e, exc_info=e)
if similarity and similarity < 70.0:
raise ValueError("QC fail: alignment to reference was less than 70%% (was %2.2f%%)" % (similarity))
diff --git a/scripts/docker/Dockerfile b/scripts/docker/Dockerfile
index 8811927..02829d4 100644
--- a/scripts/docker/Dockerfile
+++ b/scripts/docker/Dockerfile
@@ -3,7 +3,7 @@ FROM debian:10
RUN apt-get update && \
apt-get -yq --no-install-recommends -o Acquire::Retries=6 install \
python3 python3-pip python3-setuptools python3-dev python-pycurl \
- clustalw python3-biopython libcurl4-openssl-dev build-essential \
+ minimap2 python3-biopython libcurl4-openssl-dev build-essential \
libssl-dev libmagic-dev python3-magic && \
apt-get clean