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| author | Pjotr Prins | 2021-01-03 11:17:29 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2021-01-03 11:17:29 +0000 |
| commit | ba4161b1660c3a67090dd3715e9862906fb1cc5f (patch) | |
| tree | a42e2fdeb6240863c0d94d6c47522687752910c8 | |
| parent | dc0fa8f015bff6381f19036a96e19e5f72314f46 (diff) | |
| download | bh20-seq-resource-ba4161b1660c3a67090dd3715e9862906fb1cc5f.tar.gz bh20-seq-resource-ba4161b1660c3a67090dd3715e9862906fb1cc5f.tar.lz bh20-seq-resource-ba4161b1660c3a67090dd3715e9862906fb1cc5f.zip | |
genbank: specimen source
| -rw-r--r-- | workflows/pull-data/genbank/genbank.py | 8 |
1 files changed, 4 insertions, 4 deletions
diff --git a/workflows/pull-data/genbank/genbank.py b/workflows/pull-data/genbank/genbank.py index 80432de..26cb5e7 100644 --- a/workflows/pull-data/genbank/genbank.py +++ b/workflows/pull-data/genbank/genbank.py @@ -28,7 +28,8 @@ Example of an output JSON: ], "collection_location": "http://www.wikidata.org/entity/Q649", "collection_date": "2020-04-17", - "collecting_institution": "N.A.Kovtun Clinical Hospital 1 of Departament of President Affairs" + "collecting_institution": "N.A.Kovtun Clinical Hospital 1 of Departament of President Affairs", + "specimen_source": ["http://purl.obolibrary.org/obo/NCIT_C155831"] }, "virus": { "virus_strain": "SARS-CoV-2/human/RUS/20200417_10/2020", @@ -145,10 +146,8 @@ def get_metadata(id, gbseq): sample.collection_date = str(date) except dateutil.parser._parser.ParserError as e: warn("No collection_date: ",str(e)) - sample.collection_date = None except AttributeError: warn("Missing collection_date") - sample.collection_date = None # --- Host info # - Homo sapiens @@ -186,7 +185,8 @@ def get_metadata(id, gbseq): 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] - + n = fetch("specimen_source", ".//GBQualifier/GBQualifier_name/[.='isolation_source']/../GBQualifier_value") + if n: sample.specimen_source = n info = { 'id': 'placeholder', |