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transform: Move annotations to _after_ accessions
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Allows overrides of accessions if there is something that we want to
manually correct in the accession links.
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joverlee521 committed Dec 19, 2024
1 parent 1e1f014 commit fcb407c
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Showing 2 changed files with 2 additions and 3 deletions.
3 changes: 1 addition & 2 deletions bin/transform-genbank
Original file line number Diff line number Diff line change
Expand Up @@ -207,8 +207,8 @@ if __name__ == '__main__':
| ParseGeographicColumnsGenbank( base / 'source-data/us-state-codes.tsv' )
| AbbreviateAuthors()
| ApplyUserGeoLocationSubstitutionRules(geoRules)
| MergeUserAnnotatedMetadata(annotations, idKey = 'genbank_accession' )
| MergeUserAnnotatedMetadata(accessions, idKey = 'genbank_accession_rev' )
| MergeUserAnnotatedMetadata(annotations, idKey = 'genbank_accession' )
| FillDefaultLocationData()
| patchUKData(args.cog_uk_accessions, args.cog_uk_metadata)
| GenbankProblematicFilter( args.problem_data,
Expand Down Expand Up @@ -301,4 +301,3 @@ if __name__ == '__main__':
strain_name = updated_strain_names_by_line_no[entry[LINE_NUMBER_KEY]]
print( '>' , strain_name , sep='' , file= fasta_OUT)
print( entry['sequence'] , file= fasta_OUT)

2 changes: 1 addition & 1 deletion bin/transform-gisaid
Original file line number Diff line number Diff line change
Expand Up @@ -182,8 +182,8 @@ if __name__ == '__main__':

pipeline = (pipeline
| ApplyUserGeoLocationSubstitutionRules(geoRules)
| MergeUserAnnotatedMetadata(annotations)
| MergeUserAnnotatedMetadata(accessions)
| MergeUserAnnotatedMetadata(annotations)
| FillDefaultLocationData()
)

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