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authorPjotr Prins2021-01-04 09:41:58 +0000
committerPjotr Prins2021-01-04 09:41:58 +0000
commitbf8f13af6f083d382b4a3900566ef5e329084cbf (patch)
tree833a5850fcf5200463a8d6d4c3fb3453bcae3134 /workflows/pull-data/genbank/ref.py
parent3593b3f6a835f6c5927cbb1cc79e3db3c5d0053a (diff)
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Removing refs. No point in guessing terms
Diffstat (limited to 'workflows/pull-data/genbank/ref.py')
-rw-r--r--workflows/pull-data/genbank/ref.py23
1 files changed, 0 insertions, 23 deletions
diff --git a/workflows/pull-data/genbank/ref.py b/workflows/pull-data/genbank/ref.py
deleted file mode 100644
index d2a377e..0000000
--- a/workflows/pull-data/genbank/ref.py
+++ /dev/null
@@ -1,23 +0,0 @@
-# ---- BELOW IS JUST FOR REFERENCE ----
-
-if field_in_yaml == 'sequencing_coverage':
- # A regular expression would be better!
- try:
- technology[field_in_yaml] = [
- float(tech_info_to_parse.replace('(average)', '').replace("reads/nt", '').
- replace('(average for 6 sequences)', '').replace(',', '.').strip(' xX>'))
- ]
- except ValueError:
- print(accession_version, "Couldn't make sense of Coverage '%s'" % tech_info_to_parse)
- pass
-
-
-elif GBQualifier_name_text == 'collected_by':
- if any([x in GBQualifier_value_text.lower() for x in ['institute', 'hospital', 'city', 'center']]):
- sample['collecting_institution'] = GBQualifier_value_text
- else:
- sample['collector_name'] = GBQualifier_value_text
-
-elif GBQualifier_name_text == 'isolation_source':
-if GBQualifier_value_text.upper() in field_to_term_to_uri_dict['ncbi_speciesman_source']:
- GBQualifier_value_text = GBQualifier_value_text.upper() # For example, in case of 'usa: wa'