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I hope to gain taxonomy info while running taxonkit and csvtk using-t, which is helpful for me to import the result into R. But R and excel seems to have trouble importing the result. Some lines such as (et al.2015) and Sedi can't be import effectively.
得到的R导入结果要么是全部集中在一行(read.csv),要么是得到超过结果的行数和列数(read.table)
Hi,
I hope to gain taxonomy info while running taxonkit and csvtk using
-t
, which is helpful for me to import the result into R. But R and excel seems to have trouble importing the result. Some lines such as (et al.2015) and Sedi can't be import effectively.得到的R导入结果要么是全部集中在一行(read.csv),要么是得到超过结果的行数和列数(read.table)
My script is as shown below:
taxonkit lineage taxid.txt -j 120 | taxonkit reformat -r NA -R 0 -j 120 | csvtk -H -t cut -f 1,3 | csvtk -H -t sep -f 2 -s ';' -R | csvtk add-header -t -n taxid,kingdom,phylum,class,order,family,genus,species | csvtk pretty -t -o taxid_out.csv
My R script is as shown below:
test2 <- read.table("taxid_out.csv",header = TRUE)
The output file I get is as follows.
taxid_out.csv
Any help will be much appreciated.
Thank you in advance,
Alena
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