diff options
Diffstat (limited to 'bh20sequploader/qc_fasta.py')
| -rw-r--r-- | bh20sequploader/qc_fasta.py | 9 |
1 files changed, 5 insertions, 4 deletions
diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py index f567f0a..814fb3e 100644 --- a/bh20sequploader/qc_fasta.py +++ b/bh20sequploader/qc_fasta.py @@ -66,7 +66,8 @@ def qc_fasta(arg_sequence, check_with_mimimap2=True): similarity = 0 try: - cmd = ["minimap2", "-c -x asm20", tmp1.name, tmp2.name] + log.debug("Trying to run minimap2") + cmd = ["minimap2", "-c", "-x", "asm20", tmp1.name, tmp2.name] logging.info("QC checking similarity to reference") logging.info(" ".join(cmd)) result = subprocess.run(cmd, stdout=subprocess.PIPE) @@ -83,9 +84,7 @@ def qc_fasta(arg_sequence, check_with_mimimap2=True): if similarity < 70.0: raise ValueError( - "QC fail for {}: alignment to reference was less than 70%% (was %2.2f%%)".format( - seqlabel, similarity - )) + f"QC fail for {seqlabel}: alignment to reference was less than 70% (was {similarity})") return "sequence.fasta" + gz, seqlabel, seq_type elif seq_type == "text/fastq": @@ -93,4 +92,6 @@ def qc_fasta(arg_sequence, check_with_mimimap2=True): sequence.detach() return "reads.fastq" + gz, seqlabel, seq_type else: + log.debug(seqlabel) + log.debug(seq_type) raise ValueError("Sequence file ({}) does not look like a DNA FASTA or FASTQ".format(arg_sequence)) |