diff options
Diffstat (limited to 'workflows/pull-data/genbank/genbank.py')
| -rw-r--r-- | workflows/pull-data/genbank/genbank.py | 36 |
1 files changed, 26 insertions, 10 deletions
diff --git a/workflows/pull-data/genbank/genbank.py b/workflows/pull-data/genbank/genbank.py index 90f5a14..80432de 100644 --- a/workflows/pull-data/genbank/genbank.py +++ b/workflows/pull-data/genbank/genbank.py @@ -52,18 +52,28 @@ Example of an output JSON: } } -Note: missing data should be None! Do not fill in other data by -'guessing'. - -When data is malformed an warning should be issued. """ def get_metadata(id, gbseq): + """This is a minimal data parser from genbank XML records. Inference + on, for example geo location, is not allowed in this function and + happens downstream. + + That is to keep the parsing simple. + + Important: missing data should be missing or None! Do not fill in + data by 'guessing'. + + When data is malformed a warning should be logged and added to the + warning list. + + """ host = types.SimpleNamespace() sample = types.SimpleNamespace() submitter = types.SimpleNamespace() technology = types.SimpleNamespace() + virus = types.SimpleNamespace() warnings = [] def warn(msg): @@ -81,13 +91,14 @@ def get_metadata(id, gbseq): sample.sample_id = id sample.database = "https://www.ncbi.nlm.nih.gov/genbank/" sample.source_database_accession = f"http://identifiers.org/insdc/{id}#sequence" - # <GBQualifier> - # <GBQualifier_name>country</GBQualifier_name> # <GBQualifier_value>USA: Cruise_Ship_1, California</GBQualifier_value> - # </GBQualifier> - sample.collection_location = "FIXME" + n = fetch("host_species", ".//GBQualifier/GBQualifier_name/[.='country']/../GBQualifier_value") + if n: sample.collection_location = n + else: warn("Missing collection_location") submitter.authors = [n.text for n in gbseq.findall(".//GBAuthor")] + if not len(submitter.authors): warn("Missing authors") + # <GBReference_journal>Submitted (28-OCT-2020) MDU-PHL, The Peter # Doherty Institute for Infection and Immunity, 792 Elizabeth # Street, Melbourne, Vic 3000, Australia @@ -103,7 +114,6 @@ def get_metadata(id, gbseq): pass except ValueError: submitter.additional_submitter_information = n - pass try: n = gbseq.find("./GBSeq_comment").text @@ -122,6 +132,7 @@ def get_metadata(id, gbseq): p = re.compile(r'.*Sequencing Technology :: ([^;]+).*') m = p.match(n) if m: technology.sample_sequencing_technology = m.group(1).strip() + else: warn("Missing sample_sequencing_technology") # --- Dates n = gbseq.find("./GBSeq_create-date") @@ -171,13 +182,18 @@ def get_metadata(id, gbseq): host.host_age = int(m.group(1)) host.host_age_unit = 'http://purl.obolibrary.org/obo/UO_0000036' # sys.exit(1) + n = fetch("virus_strain", ".//GBQualifier/GBQualifier_name/[.='isolate']/../GBQualifier_value") + if n: virus.virus_strain = n + n = fetch("virus_species", ".//GBQualifier/GBQualifier_name/[.='db_xref']/../GBQualifier_value") + if n: virus.virus_species = "http://purl.obolibrary.org/obo/NCBITaxon_"+n.split('taxon:')[1] + info = { 'id': 'placeholder', 'update_date': str(update_date), 'host': host.__dict__, 'sample': sample.__dict__, - #'virus': virus, + 'virus': virus.__dict__, 'technology': technology.__dict__, 'submitter': submitter.__dict__, 'warnings': warnings, |