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npolar / marine-db

https://doi.org/10.21334/marine-db
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Update functional groups #22

Closed cnrdh closed 2 years ago

cnrdh commented 5 years ago

NDJSON of updated taxon-db from #21 

ndjson-cat data/deposit/taxonomy/taxon-db.json | ndjson-split > data/input/taxonomy/taxon-db.ndjson

./bin/ndjson-from-csv < data/deposit/taxonomy/functional-groups.tsv | ndjson-map '{name: d.species}' > /tmp/func-names.ndjson

cat data/input/taxonomy/taxon-db.ndjson | ndjson-map 'd.taxon || d.canonicalName' | sort | uniq | ndjson-map '{ name: d}' > /tmp/names.ndjson
~/npolar/marine-db$ ndjson-join --right 'd.name' /tmp/names.ndjson /tmp/func-names.ndjson | grep null
[null,{"name":"Coxiella pseudoannulata"}]
[null,{"name":"Gymnodinium gaelatum"}]
[null,{"name":"Gymnodinium gracilientum"}]
[null,{"name":"Karenia brevis"}]
[null,{"name":"Protherythropsis vigilans"}]
[null,{"name":"Chaetoceros convulutus"}]
[null,{"name":"Pseudo-nitzschia pseudodelicatisima"}]
cnrdh commented 5 years ago

There's some duplication in functional-groups, only difference is "cyst" 2 [{"name":"Chaetoceros furcellatus"},{"name":"Chaetoceros furcellatus"}] 2 [{"name":"Dinobryon"},{"name":"Dinobryon"}] 2 [{"name":"Dinoflagellata"},{"name":"Dinoflagellata"}] 2 [{"name":"Eutreptiella"},{"name":"Eutreptiella"}] 2 [{"name":"Rhizosolenia hebetata"},{"name":"Rhizosolenia hebetata"}]

cnrdh commented 5 years ago

@todo Typos in functional-groups.tsv needs to be corrected...