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-rw-r--r--workflows/pull-data/genbank/genbank.py24
-rw-r--r--workflows/pull-data/genbank/ref.py35
2 files changed, 11 insertions, 48 deletions
diff --git a/workflows/pull-data/genbank/genbank.py b/workflows/pull-data/genbank/genbank.py
index 5ba1ef6..2d46f3d 100644
--- a/workflows/pull-data/genbank/genbank.py
+++ b/workflows/pull-data/genbank/genbank.py
@@ -51,6 +51,10 @@ Example of an output JSON:
"submitter_address": "Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow 117997, Russia"
}
}
+
+Note: missing data should be None! Do not fill in other data by
+'guessing'.
+
"""
def get_metadata(id, gbseq):
@@ -73,29 +77,23 @@ def get_metadata(id, gbseq):
# </GBQualifier>
sample.collection_location = "FIXME"
- # --- Handling dates ---
- # <GBSeq_create-date>29-JUL-2020</GBSeq_create-date>
+ submitter.authors = [n.text for n in gbseq.findall(".//GBAuthor")]
+
+ # --- Dates
n = gbseq.find("./GBSeq_create-date")
creation_date = dateparse(n.text).date()
-
- # <GBSeq_update-date>30-JUL-2020</GBSeq_update-date>
n = gbseq.find("./GBSeq_update-date")
update_date = dateparse(n.text).date()
-
- # <GBQualifier>
- # <GBQualifier_name>collection_date</GBQualifier_name>
- # <GBQualifier_value>2020-04-01</GBQualifier_value>
- # </GBQualifier>
n = gbseq.find(".//GBQualifier/GBQualifier_name/[.='collection_date']/../GBQualifier_value")
try:
date = dateparse(n.text).date()
sample.collection_date = str(date)
except dateutil.parser._parser.ParserError as e:
- warn(str(e))
- sample.collection_date = str(creation_date)
+ warn("No collection_date: ",str(e))
+ sample.collection_date = None
except AttributeError:
- warn("Missing collection_date - used creation_date instead")
- sample.collection_date = str(creation_date)
+ warn("Missing collection_date")
+ sample.collection_date = None
info = {
'id': 'placeholder',
diff --git a/workflows/pull-data/genbank/ref.py b/workflows/pull-data/genbank/ref.py
index f803112..e998d37 100644
--- a/workflows/pull-data/genbank/ref.py
+++ b/workflows/pull-data/genbank/ref.py
@@ -1,40 +1,5 @@
# ---- BELOW IS JUST FOR REFERENCE ----
-
-min_len_to_count = 15000
-num_seq_with_len_ge_X_bp = 0
-
-missing_value_list = []
-not_created_accession_dict = {}
-accession_with_errors_list = []
-if None:
-
- tree = ET.parse(path_metadata_xxx_xml)
- GBSet = tree.getroot()
-
- for GBSeq in GBSet:
- accession_version = GBSeq.find('GBSeq_accession-version').text
-
- try:
- info = {
- 'id': 'placeholder',
- 'host': {},
- 'sample': {},
- 'virus': {},
- 'technology': {},
- 'submitter': {}
- }
-
- sample['sample_id'] = accession_version
- sample['source_database_accession'] = ["http://identifiers.org/insdc/"+accession_version+"#sequence"] #accession is turned into resolvable URL/URI now
-
- # submitter info
- GBSeq_references = GBSeq.find('GBSeq_references')
- if GBSeq_references is not None:
- author_list = ["{}".format(x.text) for x in GBSeq_references.iter('GBAuthor')]
- if len(author_list) > 0:
- submitter['authors'] = author_list
-
GBReference = GBSeq_references.find('GBReference')
if GBReference is not None:
GBReference_journal = GBReference.find('GBReference_journal')