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| author | Pjotr Prins | 2021-01-03 08:05:51 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2021-01-03 08:05:51 +0000 |
| commit | a5ba1a8062e7116c2951762f86a6ae6d1638261d (patch) | |
| tree | 6315a062ff00e72e791e68d1fb7fd75ea47a9560 /workflows/pull-data/genbank/genbank.py | |
| parent | d55a1b6556e6cd6e09405cb1f4bcf58d52892331 (diff) | |
| download | bh20-seq-resource-a5ba1a8062e7116c2951762f86a6ae6d1638261d.tar.gz bh20-seq-resource-a5ba1a8062e7116c2951762f86a6ae6d1638261d.tar.lz bh20-seq-resource-a5ba1a8062e7116c2951762f86a6ae6d1638261d.zip | |
genbank: submitter info
Diffstat (limited to 'workflows/pull-data/genbank/genbank.py')
| -rw-r--r-- | workflows/pull-data/genbank/genbank.py | 16 |
1 files changed, 16 insertions, 0 deletions
diff --git a/workflows/pull-data/genbank/genbank.py b/workflows/pull-data/genbank/genbank.py index 2d46f3d..8f6ba06 100644 --- a/workflows/pull-data/genbank/genbank.py +++ b/workflows/pull-data/genbank/genbank.py @@ -78,6 +78,22 @@ def get_metadata(id, gbseq): sample.collection_location = "FIXME" submitter.authors = [n.text for n in gbseq.findall(".//GBAuthor")] + # <GBReference_journal>Submitted (28-OCT-2020) MDU-PHL, The Peter + # Doherty Institute for Infection and Immunity, 792 Elizabeth + # Street, Melbourne, Vic 3000, Australia + # </GBReference_journal> + try: + n = gbseq.find(".//GBReference_journal").text + # print(n,file=sys.stderr) + if n != 'Unpublished': + institute,address = n.split(',',1) + submitter.submitter_name = institute.split(') ')[1] + submitter.submitter_address = address.strip() + except AttributeError: + pass + except ValueError: + submitter.additional_submitter_information = n + pass # --- Dates n = gbseq.find("./GBSeq_create-date") |