Update BOLD_web_hack.R #19
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+ Option to use Bold's Species Level Barcode Records database by setting db = "sp" * "OTU <- sub(...)" now gives "OTU1234"; previously it gave "Query: OTU1234" - object whois_num removed, because it wasn't used anywhere in the code and it was identical with whois
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input+output.zip
db = "sp". With default options (db="all") it should work just as original code does. Withdb="sp", the script expects input in format of species level database.*see attachment for input and output of
Bold_web_hack("BOLDtest.txt",db="sp")*if db is messed up, you either get an error or table full of NAs
Other minor optimizing changes are:
write.csv(temp_tab,...)is after theif, instead of two inside theifOTU <- sub(...)now gives "OTU_1234"; previously it gave "Query: OTU_1234"whois_numremoved, because it wasn't used anywhere in the code and it was identical withwhois