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Update geo synonyms to catch Newcastle parsing issue

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trvrb committed Jan 6, 2019
1 parent 08319ba commit abfc3102b9030d06b940fa7ddb1cda176fa988e2
Showing with 5 additions and 2 deletions.
  1. +1 −1 builds/FLU.md
  2. +4 −1 source-data/geo_synonyms.tsv
@@ -14,7 +14,7 @@
* `DNA Accession no. | Isolate name | Isolate ID | Segment | Passage details/history | Submitting lab`
2. Move files to `fauna/data` as `gisaid_epiflu.xls` and `gisaid_epiflu.fasta`.
3. Upload to vdb database
* `python vdb/flu_upload.py -db vdb -v flu --source gisaid --fname gisaid_epiflu`
* `python2 vdb/flu_upload.py -db vdb -v flu --source gisaid --fname gisaid_epiflu`
* Recommend running with `--preview` to confirm strain names and locations are correctly parsed before uploading
* Can add to [geo_synonyms file](source-data/geo_synonyms.tsv), [flu_strain_name_fix file](source-data/flu_strain_name_fix.tsv) and [flu_fix_location_label file](source-data/flu_fix_location_label.tsv) to fix some of the formatting.

@@ -2555,7 +2555,10 @@ MilfordHaven UnitedKingdom Wales MilfordHaven
Minehead UnitedKingdom England Minehead
Monmouth UnitedKingdom Wales Monmouth
Neath UnitedKingdom Wales Neath
NewcastleuponTyne UnitedKingdom England Newcastle
Newcastleunderlyme UnitedKingdom England Newcastleunderlyme
Newcastle-Under-Lyme UnitedKingdom England Newcastleunderlyme
Newcastleupontyne UnitedKingdom England Newcastleupontyne
Newcastle-Upon-Tyne UnitedKingdom England Newcastleupontyne
Newport UnitedKingdom Wales Newport
Ni UnitedKingdom NorthernIreland Belfast
Nib UnitedKingdom UnitedKingdom UnitedKingdom

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