diff options
Diffstat (limited to 'bh20sequploader')
| -rw-r--r-- | bh20sequploader/main.py | 9 | ||||
| -rw-r--r-- | bh20sequploader/qc_fasta.py | 64 |
2 files changed, 36 insertions, 37 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index 8555e2b..fd0278d 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -23,14 +23,16 @@ ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462' UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa' def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True): + failed = False try: log.debug("Checking metadata" if do_qc else "Skipping metadata check") if do_qc and not qc_metadata(metadata.name): - raise Exception("Failed metadata qc") + log.warning("Failed metadata qc") + failed = True except Exception as e: log.debug(e) print(e) - exit(1) + failed = True target = [] try: @@ -43,6 +45,9 @@ def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True): except Exception as e: log.debug(e) print(e) + failed = True + + if failed: exit(1) return target diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py index 8c6ebd3..37eb4e8 100644 --- a/bh20sequploader/qc_fasta.py +++ b/bh20sequploader/qc_fasta.py @@ -58,42 +58,36 @@ def qc_fasta(arg_sequence, check_with_clustalw=True): return ("sequence.fasta"+gz, seqlabel) with tempfile.NamedTemporaryFile() as tmp1: - refstring = pkg_resources.resource_string(__name__, "SARS-CoV-2-reference.fasta") - tmp1.write(refstring) - tmp1.write(submitlabel.encode("utf8")) - tmp1.write(("".join(submitseq)).encode("utf8")) - tmp1.flush() - subbp = 0 - refbp = 0 - similarity = 0 - try: - cmd = ["clustalw", "-infile="+tmp1.name, - "-quicktree", "-iteration=none", "-type=DNA"] - print("QC checking similarity to reference") - print(" ".join(cmd)) - result = subprocess.run(cmd, stdout=subprocess.PIPE) - res = result.stdout.decode("utf-8") - g1 = re.search(r"^Sequence 1: [^ ]+ +(\d+) bp$", res, flags=re.MULTILINE) - refbp = float(g1.group(1)) - g2 = re.search(r"^Sequence 2: [^ ]+ +(\d+) bp$", res, flags=re.MULTILINE) - subbp = float(g2.group(1)) - g3 = re.search(r"^Sequences \(1:2\) Aligned\. Score: (\d+(\.\d+)?)$", res, flags=re.MULTILINE) - similarity = float(g3.group(1)) + 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) - print(g1.group(0)) - print(g2.group(0)) - print(g3.group(0)) - except Exception as e: - logging.warn("QC against reference sequence using 'clustalw': %s", e) - - if refbp and (subbp/refbp) < .7: - raise ValueError("QC fail: submit sequence length is shorter than 70% reference") - if refbp and (subbp/refbp) > 1.3: - raise ValueError("QC fail: submit sequence length is greater than 130% reference") - if similarity and similarity < 70.0: - raise ValueError("QC fail: submit similarity is less than 70%") - if refbp == 0 or similarity == 0: - raise ValueError("QC fail") + if similarity and 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": |