Update BOLD_web_hack.R#19
Open
OndroV wants to merge 1 commit into
Open
Conversation
+ 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
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
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