diff options
Diffstat (limited to 'bh20sequploader')
| -rw-r--r-- | bh20sequploader/main.py | 13 | ||||
| -rw-r--r-- | bh20sequploader/qc_metadata.py | 2 |
2 files changed, 11 insertions, 4 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index 80c33c8..d2a6c5f 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -26,11 +26,14 @@ VALIDATED_PROJECT='lugli-j7d0g-5ct8p1i1wrgyjvp' def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True): failed = False + sample_id = '' try: log.debug("Checking metadata" if do_qc else "Skipping metadata check") - if do_qc and not qc_metadata(metadata.name): - log.warning("Failed metadata QC") - failed = True + if do_qc: + sample_id = qc_metadata(metadata.name) + if not sample_id: + log.warning("Failed metadata QC") + failed = True except Exception as e: log.exception("Failed metadata QC") failed = True @@ -46,6 +49,10 @@ def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True): target[0] = ("reads_1."+target[0][0][6:], target[0][1]) target[1] = ("reads_2."+target[1][0][6:], target[0][1]) + + if target[0][2] == 'text/fasta' and sample_id != target[0][1]: + raise ValueError("The sample_id field in the metadata must be the same as the FASTA header") + except Exception as e: log.exception("Failed sequence QC") failed = True diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py index 27657b1..87fa0b3 100644 --- a/bh20sequploader/qc_metadata.py +++ b/bh20sequploader/qc_metadata.py @@ -39,4 +39,4 @@ def qc_metadata(metadatafile): if not rslt: raise Exception(reason) - return True + return metadata['sample']['sample_id'] |