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| author | Peter Amstutz | 2020-07-16 21:24:05 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-07-16 21:24:05 -0400 |
| commit | b1750731b654be3322a6793f47d52fafcaaea9ac (patch) | |
| tree | 4f49aa6539b45c9c72db8e015c2413afa61a8ae8 | |
| parent | eb3bdab1109959deb5b11fd74310832bdaa50899 (diff) | |
| download | bh20-seq-resource-b1750731b654be3322a6793f47d52fafcaaea9ac.tar.gz bh20-seq-resource-b1750731b654be3322a6793f47d52fafcaaea9ac.tar.lz bh20-seq-resource-b1750731b654be3322a6793f47d52fafcaaea9ac.zip | |
Report similarity == 0
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
| -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: |