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| author | Pjotr Prins | 2021-01-04 09:41:58 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2021-01-04 09:41:58 +0000 |
| commit | bf8f13af6f083d382b4a3900566ef5e329084cbf (patch) | |
| tree | 833a5850fcf5200463a8d6d4c3fb3453bcae3134 /workflows/pull-data/genbank/ref.py | |
| parent | 3593b3f6a835f6c5927cbb1cc79e3db3c5d0053a (diff) | |
| download | bh20-seq-resource-bf8f13af6f083d382b4a3900566ef5e329084cbf.tar.gz bh20-seq-resource-bf8f13af6f083d382b4a3900566ef5e329084cbf.tar.lz bh20-seq-resource-bf8f13af6f083d382b4a3900566ef5e329084cbf.zip | |
Removing refs. No point in guessing terms
Diffstat (limited to 'workflows/pull-data/genbank/ref.py')
| -rw-r--r-- | workflows/pull-data/genbank/ref.py | 23 |
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' |