aboutsummaryrefslogtreecommitdiff
path: root/bh20sequploader/qc_fasta.py
diff options
context:
space:
mode:
authorPeter Amstutz2020-07-07 20:41:11 +0000
committerPeter Amstutz2020-07-07 20:41:11 +0000
commit54e0ce85ef3abafb8870ef5a9244a03f16b5e3f5 (patch)
tree69373d65f2355e1b1528f94c133ad5df9ed7cf92 /bh20sequploader/qc_fasta.py
parent7cf561c1b92a44d488d36dd3d883750b261c6550 (diff)
downloadbh20-seq-resource-54e0ce85ef3abafb8870ef5a9244a03f16b5e3f5.tar.gz
bh20-seq-resource-54e0ce85ef3abafb8870ef5a9244a03f16b5e3f5.tar.lz
bh20-seq-resource-54e0ce85ef3abafb8870ef5a9244a03f16b5e3f5.zip
minimap2 returns nothing when there is no alignment.
Diffstat (limited to 'bh20sequploader/qc_fasta.py')
-rw-r--r--bh20sequploader/qc_fasta.py15
1 files changed, 9 insertions, 6 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))