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Brant Faircloth edited this page Mar 20, 2020 · 2 revisions

How to select samples for species level

go to whatever directory you need to on @chili

start up database and in database (this example is for Galliformes), run:

\copy (select ordr as "Order", family as "Family", genus as "Genus", concat(genus, ' ', species) as "Genus species", authority as "Authority", common as "Common", extinct as "Extinct", '' as "Status" from species where ordr='Galliformes') TO 'galliformes.csv' CSV HEADER;

this creates an output csv file. we can pull the species level records for this order by running:

python /opt/local/bin/database/database/get_tissue_holdings_v2.py --species-spreadsheet galliformes.csv --species-excludes type-genera-to-skip.csv