diff options
Diffstat (limited to 'bh20sequploader/qc_fasta.py')
| -rw-r--r-- | bh20sequploader/qc_fasta.py | 62 |
1 files changed, 30 insertions, 32 deletions
diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py index 0c7e16d..e5c039e 100644 --- a/bh20sequploader/qc_fasta.py +++ b/bh20sequploader/qc_fasta.py @@ -25,7 +25,7 @@ def read_fasta(sequence): raise ValueError("FASTA file contains multiple entries") return label, bases -def qc_fasta(arg_sequence, check_with_clustalw=True): +def qc_fasta(arg_sequence, check_with_mimimap2=True): log.debug("Starting qc_fasta") schema_resource = pkg_resources.resource_stream(__name__, "validation/formats") with tempfile.NamedTemporaryFile() as tmp: @@ -54,38 +54,36 @@ def qc_fasta(arg_sequence, check_with_clustalw=True): sequence.seek(0) sequence.detach() - if not check_with_clustalw: - return ("sequence.fasta"+gz, seqlabel) + if check_with_mimimap2: + with tempfile.NamedTemporaryFile() as tmp1: + with tempfile.NamedTemporaryFile() as tmp2: + refstring = pkg_resources.resource_string(__name__, "SARS-CoV-2-reference.fasta") + tmp1.write(refstring) + tmp1.flush() + tmp2.write(submitlabel.encode("utf8")) + tmp2.write(("".join(submitseq)).encode("utf8")) + tmp2.flush() + subbp = 0 + refbp = 0 + similarity = 0 + try: + cmd = ["minimap2", "-c", tmp1.name, tmp2.name] + 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") + 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, exc_info=e) - with tempfile.NamedTemporaryFile() as tmp1: - with tempfile.NamedTemporaryFile() as tmp2: - refstring = pkg_resources.resource_string(__name__, "SARS-CoV-2-reference.fasta") - tmp1.write(refstring) - tmp1.flush() - tmp2.write(submitlabel.encode("utf8")) - tmp2.write(("".join(submitseq)).encode("utf8")) - tmp2.flush() - subbp = 0 - refbp = 0 - similarity = 0 - try: - cmd = ["minimap2", "-c", tmp1.name, tmp2.name] - 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") - 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, exc_info=e) - - if similarity < 70.0: - raise ValueError("QC fail: alignment to reference was less than 70%% (was %2.2f%%)" % (similarity)) + if similarity < 70.0: + raise ValueError("QC fail: alignment to reference was less than 70%% (was %2.2f%%)" % (similarity)) return ("sequence.fasta"+gz, seqlabel) elif seq_type == "text/fastq": |