scripts/extract_from_strain.py is used to extract information from strain names. Specifically with the current data, it extracts a more accurate collection year for 35 samples. The full output can be found in any recent run of Ingest to phylogenetic.
'PP_000N5LB': date '2015-XX-XX' → '2001-XX-XX'
'PP_000N73A': date '2015-XX-XX' → '2001-XX-XX'
'PP_000N748': date '2015-XX-XX' → '2001-XX-XX'
…
All 35 collection date inaccuracies have already been reported in pathoplexus/curation_reports#7. Once Pathoplexus is updated with the corrected dates, it should be safe to remove this script and simplify the workflow.
scripts/extract_from_strain.py is used to extract information from strain names. Specifically with the current data, it extracts a more accurate collection year for 35 samples. The full output can be found in any recent run of Ingest to phylogenetic.
All 35 collection date inaccuracies have already been reported in pathoplexus/curation_reports#7. Once Pathoplexus is updated with the corrected dates, it should be safe to remove this script and simplify the workflow.