diff options
Diffstat (limited to 'workflows/pull-data/genbank/genbank.py')
| -rw-r--r-- | workflows/pull-data/genbank/genbank.py | 48 |
1 files changed, 44 insertions, 4 deletions
diff --git a/workflows/pull-data/genbank/genbank.py b/workflows/pull-data/genbank/genbank.py index 314f50d..90f5a14 100644 --- a/workflows/pull-data/genbank/genbank.py +++ b/workflows/pull-data/genbank/genbank.py @@ -70,6 +70,13 @@ def get_metadata(id, gbseq): print(f"WARNING: {msg}",file=sys.stderr) warnings.append(msg) + def fetch(msg, xpath): + try: + n = gbseq.find(xpath).text + return n + except AttributeError: + warn("Missing "+msg) + host.host_species = "http://purl.obolibrary.org/obo/NCBITaxon_9606" sample.sample_id = id sample.database = "https://www.ncbi.nlm.nih.gov/genbank/" @@ -132,14 +139,47 @@ def get_metadata(id, gbseq): warn("Missing collection_date") sample.collection_date = None + # --- Host info + # - Homo sapiens + # - Homo sapiens; female + # - Homo sapiens; female 63 + # - Homo sapiens; female; age 40 + # - Homo sapiens; gender: F; age: 61 + # - Homo sapiens; gender: M; age: 68 + # - Homo sapiens; hospitalized patient + # - Homo sapiens; male + # - Homo sapiens; male; 63 + # - Homo sapiens; male; age 29 + # - Homo sapiens; symptomatic + n = fetch("host_species", ".//GBQualifier/GBQualifier_name/[.='host']/../GBQualifier_value") + if n: + list = n.split('; ') + species = list[0] + host.host_species = species + if species != "Homo sapiens": + warn(f"Species not understood: {species}") + if len(list)>1: + sex = list[1] + if 'male' in sex or 'gender: M' in sex: host.host_sex = 'male' + if 'female' in sex or 'gender: F' in sex: host.host_sex = 'female' + if len(list)>2: + age = list[2] + p = re.compile(r'[^\d]+(\d+)') + m = p.match(n) + print(m.group(1)) + if m: + host.host_age = int(m.group(1)) + host.host_age_unit = 'http://purl.obolibrary.org/obo/UO_0000036' + # sys.exit(1) + info = { 'id': 'placeholder', 'update_date': str(update_date), - 'host': host, - 'sample': sample, + 'host': host.__dict__, + 'sample': sample.__dict__, #'virus': virus, - 'technology': technology, - 'submitter': submitter, + 'technology': technology.__dict__, + 'submitter': submitter.__dict__, 'warnings': warnings, } print(info) |