diff options
Diffstat (limited to 'bh20sequploader/qc_fasta.py')
| -rw-r--r-- | bh20sequploader/qc_fasta.py | 15 |
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)) |