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authorAndreaGuarracino2020-10-01 22:36:44 +0200
committerAndreaGuarracino2020-10-01 22:36:44 +0200
commitcc9aff0931aa1579c47c01dfa74022807548b40f (patch)
treebac5a04d0da4c9bc08be745b997a957eacfc38ae /bh20sequploader/qc_fasta.py
parentb3a671f04743dc2bf48049b413d7d1f20d31bbcf (diff)
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Diffstat (limited to 'bh20sequploader/qc_fasta.py')
-rw-r--r--bh20sequploader/qc_fasta.py11
1 files changed, 7 insertions, 4 deletions
diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py
index 215d6fd..58ca22e 100644
--- a/bh20sequploader/qc_fasta.py
+++ b/bh20sequploader/qc_fasta.py
@@ -82,12 +82,15 @@ def qc_fasta(arg_sequence, check_with_mimimap2=True):
logging.warn("QC against reference sequence using 'minimap2': %s", e, exc_info=e)
if similarity < 70.0:
- raise ValueError("QC fail: alignment to reference was less than 70%% (was %2.2f%%)" % (similarity))
+ raise ValueError(
+ "QC fail for {}: alignment to reference was less than 70%% (was %2.2f%%)".format(
+ seqlabel, similarity
+ ))
- return ("sequence.fasta"+gz, seqlabel, seq_type)
+ return "sequence.fasta" + gz, seqlabel, seq_type
elif seq_type == "text/fastq":
sequence.seek(0)
sequence.detach()
- return ("reads.fastq"+gz, seqlabel, seq_type)
+ return "reads.fastq" + gz, seqlabel, seq_type
else:
- raise ValueError("Sequence file does not look like a DNA FASTA or FASTQ")
+ raise ValueError("Sequence file ({}) does not look like a DNA FASTA or FASTQ".format(arg_sequence))