diff options
| -rw-r--r-- | bh20sequploader/qc_fasta.py | 4 | ||||
| -rw-r--r-- | scripts/cleanup.py | 7 |
2 files changed, 6 insertions, 5 deletions
diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py index 37eb4e8..0c7e16d 100644 --- a/bh20sequploader/qc_fasta.py +++ b/bh20sequploader/qc_fasta.py @@ -84,10 +84,8 @@ def qc_fasta(arg_sequence, check_with_clustalw=True): except Exception as e: logging.warn("QC against reference sequence using 'minimap2': %s", e, exc_info=e) - if similarity and similarity < 70.0: + if 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": diff --git a/scripts/cleanup.py b/scripts/cleanup.py index 6a82659..78f34c8 100644 --- a/scripts/cleanup.py +++ b/scripts/cleanup.py @@ -9,11 +9,14 @@ delete_patterns = [ "%missing%`host_species`%", "%QC fail: alignment%", "%does not look like a valid URI%", - "%Duplicate of%" + "%Duplicate of%", + "%No matching triples found for predicate obo:NCIT_C42781%", + "%does not look like a valid URI%" ] revalidate_patterns = [ - "%missing%`license`%" + "%missing%`license`%", + "%QC fail%" ] for p in delete_patterns: |